Calculation Of Reduction Potentials Research Articles

An assessment of long‐range corrected density functional approximations in the calculation of the reduction potentials of Ni(S2C2H2)2, Ni(Se2C2H2)2, Ni(S2C2H2)(N2C2H4), and Ni(Se2C2H2)(N2C2H4) complexes

AbstractHerein an assessment of several long range corrected (LRC) density functional theory (DFT) methods for the calculation of reduction potentials of the ([Ni(X2C2H2)2]n/[Ni(X2C2H2)2]n−1), and ([Ni(X2C2H2)(N2C2H4)]n/[Ni(X2C2H2)(N2C2H4)]n−1) and (where X = S or Se and n = 0, or −1) redox couples was done. From the results the values of ω that provide best agreement with CCSD(T) for the tested LRC DFT methods are 0.05, 0.15, 0.05, and 0.20 bohr−1 for ω‐B97XD, LC‐BLYP, CAM‐B3LYP, and ω‐B97, respectively. With these values the unsigned average in error was 0.12 V with a SD of 0.13 V for ω‐B97XD. For LC‐BLYP, CAM‐B3LYP, and ω‐B97 the unsigned averages in relative errors were 0.12, 0.11, and 0.13 V, respectively, with respective SDs of 0.11, 0.12, and 0.13 V.

From Synthetic to Biological Fe4 S4 Complexes: Redox Properties Correlated to Function of Radical S-Adenosylmethionine Enzymes.

By employing the computational protocol for calculation of reduction potentials of the Fe4 S4 -containing species validated using a representative series of well-defined synthetic complexes, we focused on redox properties of two prototypical radical SAM enzymes to reveal how they transform SAM into the reactive 5'-deoxyadenosyl radical, and how they tune this radical for its proper biological function. We found the reduction potential of SAM is indeed elevated by 0.3-0.4 V upon coordination to Fe4 S4 , which was previously speculated in the literature. This makes a generation of 5'-deoxyadenosyl radical from SAM less endergonic (by ca. 7-9 kcal mol-1 ) and hence more feasible in both enzymes as compared to the identical process in water. Furthermore, our calculations indicate that the enzyme-bound 5'-deoxyadenosyl radical has a significantly lower reduction potential than in referential aqueous solution, which may help the enzymes to suppress potential side redox reactions and simultaneously elevate its proton-philic character, which may, in turn, promote the radical hydrogen-atom abstraction ability.

Расчет стандартных электродных потенциалов электрохимического восстановления ванадиевых соединений: подбор функционала плотности

A systematic benchmark study was performed for the first time to investigate the performance of density functional theory for calculation of reduction potentials of vanadium compounds. Six density functionals of different types were selected for testing: local OLYP and M06L, global hybrid O3LYP and B3LYP, as well as, meta-hybrid functionals TPSSh and M06. Local and hybrid functionals with a relatively high contribution of Hartree-Fock exchange showed unsatisfactory results. In particular, the widely used hybrid functional B3LYP for the transformation VIII→VII occurring in the vanadium redox flow battery yields a negative value of the standard potential instead of a positive one. Among the tested functionals the smallest deviation from the experimental data provides the meta-hybrid functional TPSSh with a 10% contribution of the Hartree-Fock exchange. The computational protocol to calculate redox potentials of vanadium compounds is suggested.

Reduction potential calculations of the Fe-S clusters in Thermus thermophilus respiratory complex I.

Respiratory complex I facilitates electron transfer from NADH to quinone over ~95 Å through a chain of seven iron-sulfur (Fe-S) clusters in the respiratory chain. In this study, the reduction potentials of the Fe-S clusters in Thermus thermophilus complex I are calculated using a Density Functional Theory + Poisson-Boltzmann method. Our results indicate that the reduction potentials are influenced by a variety of factors including the clusters being deeply buried in the complex and the protonation state of buried ionizable residues. In addition, as several of the ionizable side chains have predicted pKa values near pH 7, relatively small structural fluctuations could lead to significant (0.2 V) shifts in the reduction potential of several of the Fe-S clusters, suggesting a dynamic mechanism for electron transfer. Moreover, the method used here is a useful computational tool to study other questions about complex I. © 2019 Wiley Periodicals, Inc.

Accurate Quantum Mechanical/Molecular Mechanical Calculations of Reduction Potentials in Azurin Variants.

Understanding the regulation mechanism and molecular determinants of the reduction potential of metalloprotein is a major challenge. An ab initio quantum mechanical/molecular mechanical (QM/MM) method combining the minimum free energy path (MFEP) and fractional number of electron (FNE) approaches has been developed in our group to simulate the redox processes of large systems. The FNE scheme provides an efficient unique description for the redox process, while the MFEP method provides improved conformational sampling on complex environments such as protein in the QM/MM calculations. The reduction potentials of wild-type and seven mutants of azurin, a type 1 copper metalloprotein, were simulated with the QM/MM-MFEP+FNE approach in this paper. A range of 350 mV for the variations of the reduction potentials of these azurin proteins was reproduced faithfully with relative errors around 20 mV. The correlation between structural interactions and reduction potentials observed in simulations provides in-depth insight into the regulation of reduction potentials, which potentially can also be very useful to the engineering of metalloprotein-based electrocatalysts in artificial photosynthesis. The excellent accuracy and efficiency of the QM/MM-MFEP+FNE approach demonstrate the potential for simulations of many electron transfer processes in condensed phases and biochemical systems.

Assessment of the isodesmic method in the calculation of standard reduction potential of copper complexes.

Molecular phenomena involving electron transfer and reduction/oxidation processes are of the utmost importance in chemistry. However, accurate computational calculations of standard reduction potentials (SRPs) for transition metal complexes are still challenging. For this reason, some computational strategies have been proposed in order to overcome the main limitations in SRP calculations for copper complexes. However, these strategies are limited to particular coordination spheres and do not represent a general methodology. In this work, we present standard reduction potential calculations for copper complexes in aqueous solution covering a wide range of coordination spheres. These calculations were performed using the M06-2X density functional, and by employing the direct and isodesmic approaches. Result analysis reveals that values obtained with the use of the isodesmic method are in better agreement with experimental values than those obtained from the direct method (mean unsigned error 0.39 V with the direct and 0.08 V with the isodesmic method). This approach provides values with errors comparable to the experimental uncertainty due to the proper cancellation of computational errors. These results strongly suggest the isodesmic approach as an adequate methodology for the calculation of SRPs for copper complexes with diverse coordination spheres. Graphical Abstract Comparison between direct and isodesmic methods in the calculation of standard reduction potentials for copper complexes using DFT methods.

Reduction Potential Calculations of the Iron-Sulfur Clusters in Respiratory Complex I

Reduction Potential Calculations of the Iron-Sulfur Clusters in Respiratory Complex I

Design of novel additives and nonaqueous solvents for lithium-ion batteries through screening of cyclic organic molecules: an ab initio study of redox potentials.

We have screened 142 cyclic organic compounds in search of novel functional additives and nonaqueous solvents for use in lithium-ion batteries through the use of ab initio calculations, and have determined redox potentials for all molecules. We have estimated the range of variation in oxidation potentials through heteroatom replacement and structure modification. By analyzing the oxidative properties of these compounds, we have shown that substituted heteroatoms and isomers in cyclic organic molecules can induce large variations of oxidation potentials more than 2.3 V. Calculations of reduction potentials show that the substituted heteroatoms, isomers, and the number of double bonds in cyclic organic molecules can change reduction potentials more than 1.7 V. Additionally, we have identified seventeen and twelve compounds that could serve as additives in eliciting film formation on cathodes and anodes, respectively. We have also identified five compounds that could function in the overcharge protection of over-lithiated layered oxide cathodes. Finally, we have identified five compounds that could serve as electrochemically stable solvents for high-voltage (>6 V vs. Li/Li(+)) applications. These inductive screenings and their analyses and findings extend our empirical knowledge into quantitative estimation in the design of materials.

On the Accuracy of Calculated Reduction Potentials of Selected Group 8 (Fe, Ru, and Os) Octahedral Complexes

The theoretical calculations of reduction potentials for the [M(H2O)6]2+/3+, [M(NH3)6]2+/3+, [M(en)3]2+/3+, [M(bipy)3]2+/3+, [M(CN)6]4–/3–, and [MCl6]4–/3– systems (M = Fe, Os, Ru) were carried out. The DFT(PBE)/def2-TZVP//DFT(PBE)/def2-SVP quantum chemical method was employed to obtain presumably accurate ionization energies, whereas the conductor-like screening model for real solvents (COSMO-RS) was selected as the most suitable method for calculations of solvation energies of the oxidized and reduced forms of the studied species. It has been shown that COSMO-RS may overcome problems related to directionality of hydrogen bonds in the second solvation sphere that previously led to errors of ∼1 V for the [Ru(H2O)6]2+ complex employing PCM-like models. Thus, most of the values for (2+) → (3+) oxidations are now within 0.1–0.2 V from the experimental data, once the anticipated spin–orbit coupling effects in Os complexes (downshifting the calculated reduction potentials by ∼0.3 V) are taken into account. The...

Exploration of density functional methods for one-electron reduction potential of nitrobenzenes

Performance of the set of density functional approaches for calculation of one-electron reduction potentials of nitroaromatic compounds was investigated. To select the most precise and affordable method, we selected a set of model molecules and investigated effects of basis set, density functional, and solvation model on the calculation of reduction potentials. It was found that the mPWB1K/TZVP method provides the most accurate gas phase electron affinity values (RMS error is 0.1 eV). This method in conjunction with the PCM (Bondi) method yields also the most accurate difference in solvation energies of neutral oxidized form and anion-radical reduced form. The final E0 values were calculated with RMS error of 0.10 V, compared with experimental values.

Kinetics of Sn electrodeposition from Sn(II)–citrate solutions

The influence of solution chemistry on the electrodeposition of Sn from Sn(II)–citrate solutions is studied. The distribution of various Sn(II)–citrate complexes and citrate ligands is calculated and the results presented as speciation diagrams. At a SnCl 2·H 2O concentration of 0.22 mol/L and citrate concentration from 0.30 mol/L to 0.66 mol/L, SnH 3L + (where L represents the tetravalent citrate ligand) is the main species at pH below about 1.2 and SnHL − is the main species at pH above about 4. Polarization studies and reduction potential calculations show that the Sn(II)–citrate complexes have similar reduction potentials at a given solution composition and pH. However, the Sn(II)–citrate complexes become more difficult to reduce with higher total citrate concentration and higher solution pH. Nevertheless, SnHL − which forms at higher pH is a favored Sn(II)–citrate complex for Sn electrodeposition due to better plated film morphology, likely as a result of its slower electroplating kinetics. Precipitates are formed from the Sn(II)–citrate solutions after adding hydrochloric acid (to lower the pH). Compositional and structural analyses indicate that the precipitates may have the formula Sn 2L.

A computational study of substituted flavylium salts and their quinonoidal conjugate-bases: S0 -> S1 electronic transition, absolute pKa and reduction potential calculations by DFT and semiempirical methods

The electronic transitions for flavylium cations and quinonoidal bases of 17 substituted flavylium salts have been studied at semiempirical and DFT (density functional theory) levels. Solvent effect on electronic spectra was included by Polarizable Continuum Model, PCM. We assigned longest-wavelength absorption maxima to HOMO ® LUMO transition. Both levels of theory gave good results for electronic transitions of flavylium cations whereas only TDDFT-PCM calculations could be used for electronic transitions of their quinonoidal bases. We also performed absolute pKa calculations of nine flavylium salts at DFT level. The pKa calculated values by our PCM parameterization gave excellent results with mean absolute deviation less than a half of one pKa unit. One-electron reduction potentials were carried out for 5 flavylium cations at DFT level. The theoretical results found were in good agreement with experimental values after adjustment for a systematic deviation.

Density functional and reduction potential calculations of Fe4S4 clusters.

Density functional theory geometry optimizations and reduction potential calculations are reported for all five known oxidation states of [Fe(4)S(4)(SCH(3))(4)](n)()(-) (n = 0, 1, 2, 3, 4) clusters that form the active sites of iron-sulfur proteins. The geometry-optimized structures tend to be slightly expanded relative to experiment, with the best comparison found in the [Fe(4)S(4)(SCH(3))(4)](2)(-) model cluster, having bond lengths 0.03 A longer on average than experimentally observed. Environmental effects are modeled with a continuum dielectric, allowing the solvent contribution to the reduction potential to be calculated. The calculated protein plus solvent effects on the reduction potentials of seven proteins (including high potential iron proteins, ferredoxins, the iron protein of nitrogenase, and the "X", "A", and "B" centers of photosystem I) are also examined. A good correlation between predicted and measured absolute reduction potentials for each oxidation state of the cluster is found, both for relative potentials within a given oxidation state and for the absolute potentials for all known couples. These calculations suggest that the number of amide dipole and hydrogen bonding interactions with the Fe(4)S(4) clusters play a key role in modulating the accessible redox couple. For the [Fe(4)S(4)](0) (all-ferrous) system, the experimentally observed S = 4 state is calculated to lie lowest in energy, and the predicted geometry and electronic properties for this state correlate well with the EXAFS and Mössbauer data. Cluster geometries are also predicted for the [Fe(4)S(4)](4+) (all-ferric) system, and the calculated reduction potential for the [Fe(4)S(4)(SCH(3))(4)](1)(-)(/0) redox couple is in good agreement with that estimated for experimental model clusters containing alkylthiolate ligands.