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Elhajj S, Gozem S. First and Second Reductions in an Aprotic Solvent: Comparing Computational and Experimental One-Electron Reduction Potentials for 345 Quinones. J Chem Theory Comput 2024; 20:6227-6240. [PMID: 38970475 PMCID: PMC11270834 DOI: 10.1021/acs.jctc.4c00602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/08/2024]
Abstract
Using reference reduction potentials of quinones recently measured relative to the saturated calomel electrode (SCE) in N,N-dimethylformamide (DMF), we benchmark absolute one-electron reduction potentials computed for 345 Q/Q•- and 265 Q•-/Q2- half-reactions using adiabatic electron affinities computed with density functional theory and solvation energies computed with four continuum solvation models: IEF-PCM, C-PCM, COSMO, and SM12. Regression analyses indicate a strong linear correlation between experimental and absolute computed Q/Q•- reduction potentials with Pearson's correlation coefficient (r) between 0.95 and 0.96 and the mean absolute error (MAE) relative to the linear fit between 83.29 and 89.51 mV for different solvation methods when the slope of the regression is constrained to 1. The same analysis for Q•-/Q2- gave a linear regression with r between 0.74 and 0.90 and MAE between 95.87 and 144.53 mV, respectively. The y-intercept values obtained from the linear regressions are in good agreement with the range of absolute reduction potentials reported in the literature for the SCE but reveal several sources of systematic error. The y-intercepts from Q•-/Q2- calculations are lower than those from Q/Q•- by around 320-410 mV for IEF-PCM, C-PCM, and SM12 compared to 210 mV for COSMO. Systematic errors also arise between molecules having different ring sizes (benzoquinones, naphthoquinones, and anthraquinones) and different substituents (titratable vs nontitratable). SCF convergence issues were found to be a source of random error that was slightly reduced by directly optimizing the solute structure in the continuum solvent reaction field. While SM12 MAEs were lower than those of the other solvation models for Q/Q•-, SM12 had larger MAEs for Q•-/Q2- pointing to a larger error when describing multiply charged anions in DMF. Altogether, the results highlight the advantages of, and further need for, testing computational methods using a large experimental data set that is not skewed (e.g., having more titratable than nontitratable substituents on different parent groups or vice versa) to help further distinguish between sources of random and systematic errors in the calculations.
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Affiliation(s)
- Sarah Elhajj
- Department of Chemistry, Georgia
State University, Atlanta, Georgia 30302, United States
| | - Samer Gozem
- Department of Chemistry, Georgia
State University, Atlanta, Georgia 30302, United States
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2
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Sakurai Y, Yamaguchi S, Yamashita T, Lu Y, Kuwabara K, Yamaguchi T, Miyake Y, Kanaori K, Watanabe S, Tajima K. Mechanisms Associated with Superoxide Radical Scavenging Reactions Involving Phenolic Compounds Deduced Based on the Correlation between Oxidation Peak Potentials and Second-Order Rate Constants Determined Using Flow-Injection Spin-Trapping EPR Methods. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:16018-16031. [PMID: 38960914 DOI: 10.1021/acs.jafc.4c02873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Flow-injection spin-trapping electron paramagnetic resonance (FI-EPR) methods that involve the use of 5,5-dimethyl-pyrroline-N-oxide (DMPO) as a spin-trapping reagent have been developed for the kinetic study of the O2•- radical scavenging reactions occurring in the presence of various plant-derived and synthetic phenolic antioxidants (Aox), such as flavonoid, pyrogallol, catechol, hydroquinone, resorcinol, and phenol derivatives in aqueous media (pH 7.4 at 25 °C). The systematically estimated second-order rate constants (ks) of these phenolic compounds span a wide range (from 4.5 × 10 to 1.0 × 106 M-1 s-1). The semilogarithm plots presenting the relationship between ks values and oxidation peak potential (Ep) values of phenolic Aox are divided into three groups (A1, A2, and B). The ks-Ep plots of phenolic Aox bearing two or three OH moieties, such as pyrogallol, catechol, and hydroquinone derivatives, belonged to Groups A1 and A2. These molecules are potent O2•- radical scavengers with ks values above 3.8 × 104 (M-1 s-1). The ks-Ep plots of all phenol and resorcinol derivatives, and a few catechol and hydroquinone derivatives containing carboxyl groups adjacent to the OH groups, were categorized into the group poor scavengers (ks < 1.6 × 103 M-1 s-1). The ks values of each group correlated negatively with Ep values, supporting the hypothesis that the O2•- radical scavenging reaction proceeds via one-electron and two-proton processes. The processes were accompanied by the production of hydrogen peroxide at pH 7.4. Furthermore, the correlation between the plots of ks and the OH proton dissociation constant (pKa•) of the intermediate aroxyl radicals (ks-pKa• plots) revealed that the second proton transfer process could potentially be the rate-determining step of the O2•- radical scavenging reaction of phenolic compounds. The ks-Ep plots provide practical information to predict the O2•- radical scavenging activity of plant-derived phenolic compounds based on those molecular structures.
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Affiliation(s)
- Yasuhiro Sakurai
- National Institute of Technology, Akashi College, Akashi, Hyogo 674-8501, Japan
- Department of Molecular Chemistry, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Shuhei Yamaguchi
- Department of Molecular Chemistry, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Tomoyuki Yamashita
- Department of Molecular Chemistry, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Yao Lu
- Department of Molecular Chemistry, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Keiko Kuwabara
- Department of Molecular Chemistry, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Tomoko Yamaguchi
- Department of Molecular Chemistry, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Yusuke Miyake
- Department of Molecular Chemistry, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Kenji Kanaori
- Department of Molecular Chemistry, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Seiya Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Ehime 790-8566, Japan
| | - Kunihiko Tajima
- Department of Molecular Chemistry, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Ehime 790-8566, Japan
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3
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Tang HM, Fan WY. Transition Metal Pyrithione Complexes (Ni, Mn, Fe, and Co) as Electrocatalysts for Proton Reduction of Acetic Acid. ACS OMEGA 2023; 8:7234-7241. [PMID: 36844539 PMCID: PMC9948554 DOI: 10.1021/acsomega.3c00412] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 06/01/2023]
Abstract
A series of mononuclear first-row transition metal pyrithione M(pyr) n complexes (M = Ni(II), Mn(II), n = 2; M = Co(III), Fe(III), n = 3) have been prepared from the reaction of the corresponding metal salt with the sodium salt of pyrithione. Using cyclic voltammetry, the complexes have been shown to behave as proton reduction electrocatalysts albeit with varying efficiencies in the presence of acetic acid as the proton source in acetonitrile. The nickel complex displays the optimal overall catalytic performance with an overpotential of 0.44 V. An ECEC mechanism is suggested for the nickel-catalyzed system based on the experimental data and supported by density functional theory calculations.
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4
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Benchmarking the Computed Proton Solvation Energy and Absolute Potential in Non-aqueous Solvents. Electrochim Acta 2023. [DOI: 10.1016/j.electacta.2022.141785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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5
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Loke WLJ, Guo W, Sohail M, Bengali AA, Fan WY. Manganese Tricarbonyl Diimine Bromide Complexes as Electrocatalysts for Proton Reduction. Inorg Chem 2022; 61:20699-20708. [DOI: 10.1021/acs.inorgchem.2c03675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Wen Liang James Loke
- Department of Chemistry, National University of Singapore, 3 Science Drive 3,117543, Singapore
| | - Wenzhuo Guo
- Department of Chemistry, National University of Singapore, 3 Science Drive 3,117543, Singapore
| | - Muhammad Sohail
- Department of Chemistry, Texas A&M University at Qatar, Doha23874, Qatar
| | - Ashfaq A. Bengali
- Department of Chemistry, Texas A&M University at Qatar, Doha23874, Qatar
| | - Wai Yip Fan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3,117543, Singapore
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6
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Busch M, Ahlberg E, Ahlberg E, Laasonen K. How to Predict the p K a of Any Compound in Any Solvent. ACS OMEGA 2022; 7:17369-17383. [PMID: 35647457 PMCID: PMC9134414 DOI: 10.1021/acsomega.2c01393] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Acid-base properties of molecules in nonaqueous solvents are of critical importance for almost all areas of chemistry. Despite this very high relevance, our knowledge is still mostly limited to the pK a of rather few compounds in the most common solvents, and a simple yet truly general computational procedure to predict pK a's of any compound in any solvent is still missing. In this contribution, we describe such a procedure. Our method requires only the experimental pK a of a reference compound in water and a few standard quantum-chemical calculations. This method is tested through computing the proton solvation energy in 39 solvents and by comparing the pK a of 142 simple compounds in 12 solvents. Our computations indicate that the method to compute the proton solvation energy is robust with respect to the detailed computational setup and the construction of the solvation model. The unscaled pK a's computed using an implicit solvation model on the other hand differ significantly from the experimental data. These differences are partly associated with the poor quality of the experimental data and the well-known shortcomings of implicit solvation models. General linear scaling relationships to correct this error are suggested for protic and aprotic media. Using these relationships, the deviations between experiment and computations drop to a level comparable to that observed in water, which highlights the efficiency of our method.
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Affiliation(s)
- Michael Busch
- Department
of Chemistry and Material Science, School of Chemical Engineering, Aalto University, Kemistintie 1, 02150 Espoo, Finland
| | - Ernst Ahlberg
- Universal
Prediction AB, 42677 Gothenburg, Sweden
- Department
of Pharmaceutical Biosciences, Uppsala University, Husargatan 3, 75124 Uppsala, Sweden
| | - Elisabet Ahlberg
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Kemigården 4, 41296 Gothenburg, Sweden
| | - Kari Laasonen
- Department
of Chemistry and Material Science, School of Chemical Engineering, Aalto University, Kemistintie 1, 02150 Espoo, Finland
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7
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Lian D, Takano Y, Shigeta Y. Evaluation of an Appropriate Standard Hydrogen Electrode Potential for Computing Redox Potentials of Catechins with Density Functional Theory. CHEM LETT 2022. [DOI: 10.1246/cl.220165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Duan Lian
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi, Asaminami-ku, Hiroshima 731-3194 Japan
- Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577 Japan
| | - Yu Takano
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi, Asaminami-ku, Hiroshima 731-3194 Japan
| | - Yasuteru Shigeta
- Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577 Japan
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577 Japan
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8
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Tang HM, Fan WY. Dithiolato-Bridged Nickel(II) Salicylcysteamine Complexes as Robust Proton Reduction Electrocatalysts: Cyclic Voltammetry and Computational Studies. Inorg Chem 2021; 60:17933-17941. [PMID: 34739253 DOI: 10.1021/acs.inorgchem.1c02524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of Schiff-base nickel(II) complexes were prepared from the reaction of nickel(II) acetate with N-salicylcysteamine [HO-C6H4-CH═N(CH2)2SH] ligands. These complexes were analyzed to be dimeric nickel complexes containing two bridging thiolato ligands. Using cyclic voltammetry, they were found to be efficient homogeneous proton reduction electrocatalysts when acetic acid was used as the proton source in acetonitrile. Catalysis was triggered upon electrochemical reduction of the nickel complex. In particular, rate constants (kobs) in the range of 104 s-1 at moderate overpotentials of 0.5-0.6 V were achieved when chloro- or bromo-containing nickel complexes were used. Combined with the experimental data, density functional theory calculations lent support to an ECEC mechanism, with the first electrochemical reduction step contributing significantly to the rate-determining step.
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Affiliation(s)
- Hui Min Tang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Wai Yip Fan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
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9
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Busch M, Ahlberg E, Laasonen K. From absolute potentials to a generalized computational standard hydrogen electrode for aqueous and non-aqueous solvents. Phys Chem Chem Phys 2021; 23:11727-11737. [PMID: 33982050 DOI: 10.1039/d1cp00499a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We describe a simple and efficient procedure to compute a conversion factor for the absolute potential of the standard hydrogen electrode in water to any other solvent. In contrast to earlier methods our procedure only requires the pKa of an arbitrary acid in water and few simple quantum chemical calculations as input. Thus, it is not affected adversely by experimental shortcomings related to measurements in non-aqueous solvents. By combining this conversion factor with the absolute potential in water, the absolute potential in the solvent of interest is obtained. Based on this procedure a new generalized computational standard hydrogen electrode for the computation of electron transfer and proton-coupled electron transfer potentials in non-aqueous solvents and ionic liquids is developed. This enables for the first time the reliable prediction of redox potentials in any solvent. The method is tested through calculation of absolute potentials in 36 solvents. Using the Kamlet-Taft linear solvation energy model we find that the relative absolute potentials consistently increase with decreasing polarisability and decreasing hydrogen bonding ability. For protic solvents good agreement with literature is observed while significant deviations are found for aprotic solvents. The obtained conversion factors are independent of the quantum chemical method, while minor differences are observed between solvation models. This does, however, not affect the global trends.
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Affiliation(s)
- Michael Busch
- Department of Chemistry and Material Science, School of Chemical Engineering, Aalto University Kemistintie 1, 02150 Espoo, Finland.
| | - Elisabet Ahlberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemigården 4, 41296 Gothenburg, Sweden
| | - Kari Laasonen
- Department of Chemistry and Material Science, School of Chemical Engineering, Aalto University Kemistintie 1, 02150 Espoo, Finland.
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10
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Fossat M, Zeng X, Pappu RV. Uncovering Differences in Hydration Free Energies and Structures for Model Compound Mimics of Charged Side Chains of Amino Acids. J Phys Chem B 2021; 125:4148-4161. [PMID: 33877835 PMCID: PMC8154595 DOI: 10.1021/acs.jpcb.1c01073] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/07/2021] [Indexed: 02/07/2023]
Abstract
Free energies of hydration are of fundamental interest for modeling and understanding conformational and phase equilibria of macromolecular solutes in aqueous phases. Of particular relevance to systems such as intrinsically disordered proteins are the free energies of hydration and hydration structures of model compounds that mimic charged side chains of Arg, Lys, Asp, and Glu. Here, we deploy a Thermodynamic Cycle-based Proton Dissociation (TCPD) approach in conjunction with data from direct measurements to obtain estimates for the free energies of hydration for model compounds that mimic the side chains of Arg+, Lys+, Asp-, and Glu-. Irrespective of the choice made for the hydration free energy of the proton, the TCPD approach reveals clear trends regarding the free energies of hydration for Arg+, Lys+, Asp-, and Glu-. These trends include asymmetries between the hydration free energies of acidic (Asp- and Glu-) and basic (Arg+ and Lys+) residues. Further, the TCPD analysis, which relies on a combination of experimental data, shows that the free energy of hydration of Arg+ is less favorable than that of Lys+. We sought a physical explanation for the TCPD-derived trends in free energies of hydration. To this end, we performed temperature-dependent calculations of free energies of hydration and analyzed hydration structures from simulations that use the polarizable Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field and water model. At 298 K, the AMOEBA model generates estimates of free energies of hydration that are consistent with TCPD values with a free energy of hydration for the proton of ca. -259 kcal/mol. Analysis of temperature-dependent simulations leads to a structural explanation for the observed differences in free energies of hydration of ionizable residues and reveals that the heat capacity of hydration is positive for Arg+ and Lys+ and negative for Asp- and Glu-.
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Affiliation(s)
| | | | - Rohit V. Pappu
- Department of Biomedical Engineering
and Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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11
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DUAN L, TAKANO Y, SHIGETA Y. Theoretical Prediction of the Redox Potential of Catechins with First Principle Calculation. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2021. [DOI: 10.2477/jccj.2022-0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Lian DUAN
- Graduate School of Information Sciences, Hiroshima City University
| | - Yu TAKANO
- Graduate School of Information Sciences, Hiroshima City University
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12
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Malloum A, Fifen JJ, Conradie J. Determination of the absolute solvation free energy and enthalpy of the proton in solutions. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114919] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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13
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Busch M, Laasonen K, Ahlberg E. Method for the accurate prediction of electron transfer potentials using an effective absolute potential. Phys Chem Chem Phys 2020; 22:25833-25840. [PMID: 33150898 DOI: 10.1039/d0cp04508j] [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
A protocol for the accurate computation of electron transfer (ET) potentials from ab initio and density functional theory (DFT) calculations is described. The method relies on experimental pKa values, which can be measured accurately, to compute a computational setup dependent effective absolute potential. The effective absolute potentials calculated using this protocol display strong variations between the different computational setups and deviate in several cases significantly from the "generally accepted" value of 4.28 V. The most accurate estimate, obtained from CCSD(T)/aug-ccpvqz, indicates an absolute potential of 4.14 V for the normal hydrogen electrode (nhe) in water. Using the effective absolute potential in combination with CCSD(T) and a moderately sized basis, we are able to predict ET potentials accurately for a test set of small organic molecules (σ = 0.13 V). Similarly we find the effective absolute potential method to perform equally good or better for all considered DFT functionals compared to using one of the literature values for the absolute potential. For, M06-2X, which comprises the most accurate DFT method, standard deviation of 0.18 V is obtained. This improved performance is a result of using the most appropriate effective absolute potential for a given method.
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Affiliation(s)
- Michael Busch
- Department of Chemistry and Material Science, School of Chemical Engineering, Aalto University Kemistintie 1, 02150 Espoo, Finland.
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14
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Triphos nickel(II) halide pincer complexes as robust proton reduction electrocatalysts. MOLECULAR CATALYSIS 2020. [DOI: 10.1016/j.mcat.2020.110950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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15
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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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16
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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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17
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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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18
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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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Matsui T, Shigeta Y, Morihashi K. Assessment of Methodology and Chemical Group Dependences in the Calculation of the pKa for Several Chemical Groups. J Chem Theory Comput 2017; 13:4791-4803. [DOI: 10.1021/acs.jctc.7b00587] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Toru Matsui
- Department
of Chemistry, Graduate School of Pure and Applied Sciences, 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
| | - Kenji Morihashi
- Department
of Chemistry, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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20
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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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21
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Gillet N, Lévy B, Moliner V, Demachy I, de la Lande A. Theoretical estimation of redox potential of biological quinone cofactors. J Comput Chem 2017; 38:1612-1621. [PMID: 28470751 DOI: 10.1002/jcc.24802] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/09/2017] [Accepted: 03/10/2017] [Indexed: 11/10/2022]
Abstract
Redox potentials are essential to understand biological cofactor reactivity and to predict their behavior in biological media. Experimental determination of redox potential in biological system is often difficult due to complexity of biological media but computational approaches can be used to estimate them. Nevertheless, the quality of the computational methodology remains a key issue to validate the results. Instead of looking to the best absolute results, we present here the calibration of theoretical redox potential for quinone derivatives in water coupling QM + MM or QM/MM scheme. Our approach allows using low computational cost theoretical level, ideal for long simulations in biological systems, and determination of the uncertainties linked to the calculations. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Natacha Gillet
- Laboratoire de Chimie-Physique, Université Paris Sud, CNRS, UMR 8000. 15, rue Jean Perrin, 91405 Orsay, CEDEX, France.,Departament de Química Física i Analítica, Universitat Jaume I, Castellón, 12071, Spain
| | - Bernard Lévy
- Laboratoire de Chimie-Physique, Université Paris Sud, CNRS, UMR 8000. 15, rue Jean Perrin, 91405 Orsay, CEDEX, France
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, Castellón, 12071, Spain.,Department of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Isabelle Demachy
- Laboratoire de Chimie-Physique, Université Paris Sud, CNRS, UMR 8000. 15, rue Jean Perrin, 91405 Orsay, CEDEX, France
| | - Aurélien de la Lande
- Laboratoire de Chimie-Physique, Université Paris Sud, CNRS, UMR 8000. 15, rue Jean Perrin, 91405 Orsay, CEDEX, France
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22
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Malloum A, Fifen JJ, Dhaouadi Z, Engo SGN, Jaidane NE. Solvation energies of the proton in ammonia explicitly versus temperature. J Chem Phys 2017; 146:134308. [DOI: 10.1063/1.4979568] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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23
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Ishikawa A, Nakai H. Quantum chemical approach for condensed-phase thermochemistry (III): Accurate evaluation of proton hydration energy and standard hydrogen electrode potential. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.03.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Hussain J, Jónsson H, Skúlason E. Faraday efficiency and mechanism of electrochemical surface reactions: CO2 reduction and H2 formation on Pt(111). Faraday Discuss 2016; 195:619-636. [DOI: 10.1039/c6fd00114a] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An atomic scale model of the electrical double layer is used to calculate the mechanism and rate of electrochemical reduction of CO2 as well as H2 formation at a Pt(111) electrode. The water layer contains solvated protons and the electrode has excess electrons at the surface. Density functional theory within the generalized gradient approximation is used to describe the electronic structure while the mechanism and activation energy of the various elementary reactions is obtained by calculating minimum energy paths using the nudged elastic band method. The applied electrical potential is deduced from the calculated work function. The optimal reaction mechanism for CO2 reduction to either methane or methanol is found and the estimated rate compared with that of the competing reaction, H2 formation. When the free energy of only the intermediates and reactants is taken into account, not the activation energy, Pt(111) would seem to be a good electrocatalyst for CO2 reduction, significantly better than Cu(111). This, however, contradicts experimental findings. Detailed calculations reported here show that the activation energy for CO2 reduction is high for both Heyrovsky and Tafel mechanisms on Pt(111) in the relevant range of applied potential. The rate-limiting step of the Heyrovsky mechanism, *COOH + H+ + e− → *CO + H2O, is estimated to have an activation energy of 0.95 eV at −0.9 V vs. standard hydrogen electrode. Under the same conditions, the activation energy for H2 formation is estimated to be only 0.5 eV. This explains why attempts to reduce CO2 using platinum electrodes have produced only H2. A comparison is made with analogous results for Cu(111) [J. Hussain et al., Procedia Comput. Sci., 2015, 51, 1865] where a reaction mechanism with low activation energy for CO2 electroreduction to methane was identified. The difference between the two electrocatalysts is discussed.
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Affiliation(s)
- Javed Hussain
- Science Institute and Faculty of Physical Sciences
- University of Iceland VR-III
- 107 Reykjavík
- Iceland
| | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences
- University of Iceland VR-III
- 107 Reykjavík
- Iceland
- Department of Applied Physics
| | - Egill Skúlason
- Science Institute and Faculty of Physical Sciences
- University of Iceland VR-III
- 107 Reykjavík
- Iceland
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25
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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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26
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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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27
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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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28
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Iwayama M, Kurniawan I, Kawaguchi K, Saito H, Nagao H. A hybrid-type approach with MD and DFT calculations for evaluation of redox potential of molecules. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1012641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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29
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Matsui T, Kitagawa Y, Okumura M, Shigeta Y. Accurate standard hydrogen electrode potential and applications to the redox potentials of vitamin C and NAD/NADH. J Phys Chem A 2015; 119:369-76. [PMID: 25514626 DOI: 10.1021/jp508308y] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We computationally evaluated the standard hydrogen electrode (SHE) potential in aqueous phase and the Gibbs energy of a proton from the experimental pKa values of alcohol molecules. From the "golden standard" CCSD(T)/aug-cc-pVTZ level calculation, we estimated the SHE potential as 4.48 V, which is very close to the IUPAC-recommended experimental value of 4.44 V. As applications to the Gaussian-3 (G3) methods, which also reproduce the "golden standard" level calculations, we computed various pKa values and redox potentials for a vitamin series. For vitamin C, we support the experimental result of +0.35 V and predict the pKa value of d-ascorbic acid to be 3.7-3.9. Using a model molecule for nicotinamide adenine dinucleotide (NAD), we reproduced the redox potential and determined the order of the proton/electron addition, based on both the proton affinity and redox potential.
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Affiliation(s)
- Toru Matsui
- Department of Chemistry, Graduate School of Science, Osaka University , 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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30
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Prediction of the reduction potential of tris(2,2′-bipyridinyl)iron(III/II) derivatives. J Comput Chem 2014; 36:33-41. [DOI: 10.1002/jcc.23766] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 09/17/2014] [Accepted: 10/06/2014] [Indexed: 11/07/2022]
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31
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Kim H, Park J, Lee YS. A protocol to evaluate one electron redox potential for iron complexes. J Comput Chem 2013; 34:2233-41. [DOI: 10.1002/jcc.23380] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 06/22/2013] [Accepted: 06/25/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Hyungjun Kim
- Department of Chemistry; KAIST; Daejeon; 305-701; Korea
| | - Joungwon Park
- Battery Group, Energy Lab, Samsung Advanced Institute of Technology; Samsung Electronics; Giheung-gu; Yongin-si; Gyeonggi-do; 446-712; Korea
| | - Yoon Sup Lee
- Department of Chemistry; KAIST; Daejeon; 305-701; Korea
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32
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Matsui T, Kitagawa Y, Shigeta Y, Okumura M. A Density Functional Theory Based Protocol to Compute the Redox Potential of Transition Metal Complex with the Correction of Pseudo-Counterion: General Theory and Applications. J Chem Theory Comput 2013; 9:2974-80. [DOI: 10.1021/ct4002653] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Toru Matsui
- Department of Chemistry, Graduate
School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka,
Osaka 560-0043, Japan
| | - Yasutaka Kitagawa
- Department of Chemistry, Graduate
School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka,
Osaka 560-0043, Japan
| | - Yasuteru Shigeta
- Department
of Materials Engineering
Science, Graduate School of Engineering Science, Osaka University,
1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
- Core Research for Evolutional
Science and Technology (CREST), Japan Science and Technology (JST)
Agency, Kawaguchi, 332-0012 Saitama, Japan
| | - Mitsutaka Okumura
- Department of Chemistry, Graduate
School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka,
Osaka 560-0043, Japan
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33
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Jono R, Sumita M, Tateyama Y, Yamashita K. Redox Reaction Mechanisms with Non-triiodide Mediators in Dye-Sensitized Solar Cells by Redox Potential Calculations. J Phys Chem Lett 2012; 3:3581-3584. [PMID: 26290992 DOI: 10.1021/jz301589a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We investigate reaction mechanisms of the redox mediators in dye-sensitized solar cells through systematic calculations of redox potentials of possible cobalt complexes and iodides in acetonitrile solution by use of the thermodynamic cycle method with continuum solvent model. The calculated redox potentials were in good agreement with the experimental values, although the experimentalists used different reference electrodes. The maximum open circuit voltage (VOC) of the mediators calculated in this work indicate that the I2(•-)/2I(-) and I2/I2(•-) as well as the net I2/2I(-) redox reactions can dominate at both photoanode and counter-electrode.
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Affiliation(s)
- Ryota Jono
- †Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Masato Sumita
- ‡International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- §CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 333-0012, Japan
| | - Yoshitaka Tateyama
- ‡International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- §CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 333-0012, Japan
- ∥PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 333-0012, Japan
| | - Koichi Yamashita
- †Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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