| 1. |
Miho Isegawa, Shigeki Kato, Electronic polarization effect on low-frequency infrared and Raman spectra of aprotic solvent: Molecular dynamics simulation study with charge response kernel by second order Moller-Plesset perturbation method, JOURNAL OF CHEMICAL PHYSICS, 10.1063/1.2813421, 127, 24, 2007.12, Low-frequency infrared (IR) and depolarized Raman scattering (DRS) spectra of acetonitrile, methylene chloride, and acetone liquids are simulated via molecular dynamics calculations with the charge response kernel (CRK) model obtained at the second order Moller-Plesset perturbation (MP2) level. For this purpose, the analytical second derivative technique for the MP2 energy is employed to evaluate the CRK matrices. The calculated IR spectra reasonably agree with the experiments. In particular, the agreement is excellent for acetone because the present CRK model well reproduces the experimental polarizability in the gas phase. The importance of interaction induced dipole moments in characterizing the spectral shapes is stressed. The DRS spectrum of acetone is mainly discussed because the experimental spectrum is available only for this molecule. The calculated spectrum is close to the experiment. The comparison of the present results with those by the multiple random telegraph model is also made. By decomposing the polarizability anisotropy time correlation function to the contributions from the permanent, induced polarizability and their cross term, a discrepancy from the previous calculations is observed in the sign of permanent-induce cross term contribution. The origin of this discrepancy is discussed by analyzing the correlation functions for acetonitrile. (C) 2007 American Institute of Physics.. |
| 2. |
Miho Isegawa, Shigeki Kato, Polarizable Force Field for Protein with Charge Response Kernel, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10.1021/ct900295u, 5, 10, 2809-2821, 2009.10, We present a molecular mechanical force field for polypeptides and proteins involving the electronic polarization effect described with the charge response kernel. All of the electrostatic parameters for 20 amino acids are obtained by ab initio electronic structure calculations and combined with the AMBER99 force field. The refittings of dihedral angle parameters in the torsional potentials are performed so as to reproduce the ab initio optimized geometries and relative energies for the conformers of dipeptides. The present force field is applied to molecular dynamics simulation calculations of the extended alanine tetra and cyclic pentapeptides in aqueous solution. The infrared spectra are calculated in order to analyze the charge polarization effect on the spectral profiles.. |
| 3. |
Miho Isegawa, Jiali Gao, Donald G. Truhlar, Incorporation of charge transfer into the explicit polarization fragment method by grand canonical density functional theory, JOURNAL OF CHEMICAL PHYSICS, 10.1063/1.3624890, 135, 8, 2011.08, Molecular fragmentation algorithms provide a powerful approach to extending electronic structure methods to very large systems. Here we present a method for including charge transfer between molecular fragments in the explicit polarization (X-Pol) fragment method for calculating potential energy surfaces. In the conventional X-Pol method, the total charge of each fragment is preserved, and charge transfer between fragments is not allowed. The description of charge transfer is made possible by treating each fragment as an open system with respect to the number of electrons. To achieve this, we applied Mermin's finite temperature method to the X-Pol wave function. In the application of this method to X-Pol, the fragments are open systems that partially equilibrate their number of electrons through a quasithermodynamics electron reservoir. The number of electrons in a given fragment can take a fractional value, and the electrons of each fragment obey the Fermi-Dirac distribution. The equilibrium state for the electrons is determined by electronegativity equalization with conservation of the total number of electrons. The amount of charge transfer is controlled by re-interpreting the temperature parameter in the Fermi-Dirac distribution function as a coupling strength parameter. We determined this coupling parameter so as to reproduce the charge transfer energy obtained by block localized energy decomposition analysis. We apply the new method to ten systems, and we show that it can yield reasonable approximations to potential energy profiles, to charge transfer stabilization energies, and to the direction and amount of charge transferred. (C) 2011 American Institute of Physics. [doi:10.1063/1.3624890]. |
| 4. |
Miho Isegawa, Roberto Peverati, Donald G. Truhlar, Performance of recent and high-performance approximate density functionals for time-dependent density functional theory calculations of valence and Rydberg electronic transition energies, JOURNAL OF CHEMICAL PHYSICS, 10.1063/1.4769078, 137, 24, 2012.12, We report a test of 30 density functionals, including several recent ones, for their predictions of 69 singlet-to-singlet excitation energies of 11 molecules. The reference values are experimental results collected by Caricato et al. for 30 valence excitations and 39 Rydberg excitations. All calculations employ time-dependent density functional theory in the adiabatic, linear-response approximation. As far as reasonable, all of the assignments are performed by essentially the same protocol as used by Caricato et al., and this allows us to merge our mean unsigned errors (MUEs) with the ones they calculated for both density functional and wave function methods. We find 21 of the 30 density functionals calculated here have smaller MUEs for the 30 valence states than what they obtained (0.47 eV) for the state-of-the-art EOM-CCSD wave function. In contrast, for all of density functionals the MUE for 39 Rydberg states is larger than that (0.11 eV) of EOM-CCSD. Merging the 30 density functionals calculated here with the 26 calculated by Caricato et al. makes a set of 56 density functionals. Averaging the unsigned errors over both the valence excitations and the Rydberg excitations, none of the 56 density functionals shows a lower mean unsigned error than that (0.27 eV) of EOM-CCSD. Nevertheless, two functionals are successful in having an overall mean unsigned error of 0.30 eV, and another nine are moderately successful in having overall mean unsigned errors in the range 0.32-0.36 eV. Successful or moderately successful density functionals include seven hybrid density functionals with 41% to 54% Hartree-Fock exchange, and four range-separated hybrid density functionals in which the percentage of Hartree-Fock exchange increases from 0% to 19% at small interelectronic separation to 65%-100% at long range. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4769078]. |
| 5. |
Miho Isegawa, Luke Fiedler, Hannah R. Leverentz, Yingjie Wang, Santhanamoorthi Nachimuthu, Jiali Gao, Donald G. Truhlar, Polarized Molecular Orbital Model Chemistry 3. The PMO Method Extended to Organic Chemistry, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10.1021/ct300509d, 9, 1, 33-45, 2013.01, The polarized molecular orbital (PMO) method, a neglect-of-diatomic-differential-overlap (NDDO) semiempirical molecular orbital method previously parametrized for systems composed of O and H, is here extended to carbon. We modified the formalism and optimized all the parameters in the PMO Hamiltonian by using a genetic algorithm and a database containing both electrostatic and energetic properties; the new parameter set is called PMO2. The quality of the resulting predictions is compared to results obtained by previous NDDO semiempirical molecular orbital methods, both including and excluding dispersion terms. We also compare the PMO2 properties to SCC-DFTB calculations. Within the class of semiempirical molecular orbital methods, the PMO2 method is found to be especially accurate for polarizabilities, atomization energies, proton transfer energies, noncovalent complexation energies, and chemical reaction barrier heights and to have good across-the-board accuracy for a range of other properties, including dipole moments, partial atomic charges, and molecular geometries.. |
| 6. |
Ruifang Li, Roberto Peverati, Miho Isegawa, Donald G. Truhar, Assessment and Validation of Density Functional Approximations for Iron Carbide and Iron Carbide Cation, JOURNAL OF PHYSICAL CHEMISTRY A, 10.1021/jp3079106, 117, 1, 169-173, 2013.01, Using quantum chemical approximations to understand and predict complex transition metal chemistry, such as catalytic processes and materials properties, is an important activity in modern computational chemistry. High-level theory can sometimes provide high-precision benchmarks for systems containing transition metals, and these benchmarks can be used to understand the reliability of less expensive quantum chemical approximations that are applicable to complex systems. Here, we studied the ionization potential energy of Fe and FeC and the bond dissociation energies of FeC and FeC+ by 15 density functional approximations: M05, M06, M06-L, omega B97, omega B97X, omega B97X-D, tau-HCTHhyb, BLYP, B3LYP, M08-HX, M08-SO, SOGGA11, SOGGA11-X, M11, and M11-L. All of the functionals predict the correct spin state as the ground state of neutral iron atom, but five of them predict the wrong spin state for Fe. In the final analysis, four functionals, namely M11-L, tau-HCTHhyb, SOGGA11, and M06-L, have small mean unsigned errors when averaged over two bond dissociation energies and two ionization potentials. In fact, the results show that M11-L gives the smallest averaged mean unsigned error, i.e., M11-L is the most reliable density functional for these iron carbide systems among those studied.. |
| 7. |
Miho Isegawa, Bo Wang, Donald G. Truhlar, Electrostatically Embedded Molecular Tailoring Approach and Validation for Peptides, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10.1021/ct300845q, 9, 3, 1381-1393, 2013.03, We add higher-order electronic polarization effects to the molecular tailoring approach (MTA) by embedding each fragment in background charges as in combined quantum mechanical and molecular mechanical (QM/MM) methods; the resulting method considered here is called electrostatically embedded MTA (EE-MTA). We compare EE-MTA to MTA for a test peptide, Ace-(Ala)(20)-NMe, and we find that including background charges (embedding charges) greatly improves the performance. The fragmentation is performed on the basis of amino acids as monomers, and several sizes of fragment are tested. The fragments are capped with either hydrogen cap atoms or tuned fluorine cap atoms. The effective core potential of the tuned fluorine cap atom is optimized so as to reproduce the proton affinity for seven types of tetrapeptide, and the proton affinity calculated with the tuned cap atom shows a lower mean unsigned error than that obtained by using a hydrogen cap atom. In the application to the test peptide, these generically tuned cap atoms show better performance compared with the hydrogen cap atom for both the electronic energy and the energy difference between an alpha helix and a beta sheet (in the latter case, 1.0% vs 2.7% when averaged over three sizes of fragments and two locations for cut bonds). Also, we compared the accuracy of several charge redistribution schemes, and we find that the results are not particularly sensitive to these choices for the Ace-(Ala)(20)-NMe peptide. We also illustrate the dependence on the choice of charge model for the embedding charges, including both fixed embedding charges and embedding charges that depend on conformation.. |
| 8. |
Miho Isegawa, Donald G. Truhlar, Valence excitation energies of alkenes, carbonyl compounds, and azabenzenes by time-dependent density functional theory: Linear response of the ground state compared to collinear and noncollinear spin-flip TDDFT with the Tamm-Dancoff approximation, JOURNAL OF CHEMICAL PHYSICS, 10.1063/1.4798402, 138, 13, 2013.04, Time-dependent density functional theory (TDDFT) holds great promise for studying photochemistry because of its affordable cost for large systems and for repeated calculations as required for direct dynamics. The chief obstacle is uncertain accuracy. There have been many validation studies, but there are also many formulations, and there have been few studies where several formulations were applied systematically to the same problems. Another issue, when TDDFT is applied with only a single exchange-correlation functional, is that errors in the functional may mask successes or failures of the formulation. Here, to try to sort out some of the issues, we apply eight formulations of adiabatic TDDFT to the first valence excitations of ten molecules with 18 density functionals of diverse types. The formulations examined are linear response from the ground state (LR-TDDFT), linear response from the ground state with the Tamm-Dancoff approximation (TDDFT-TDA), the original collinear spin-flip approximation with the Tamm-Dancoff (TD) approximation (SF1-TDDFT-TDA), the original noncollinear spin-flip approximation with the TDA approximation (SF1-NC-TDDFT-TDA), combined self-consistent-field (SCF) and collinear spin-flip calculations in the original spin-projected form (SF2-TDDFT-TDA) or non-spin-projected (NSF2-TDDFT-TDA), and combined SCF and noncollinear spin-flip calculations (SF2-NC-TDDFT-TDA and NSF2-NC-TDDFT-TDA). Comparing LR-TDDFT to TDDFT-TDA, we observed that the excitation energy is raised by the TDA; this brings the excitation energies underestimated by full linear response closer to experiment, but sometimes it makes the results worse. For ethylene and butadiene, the excitation energies are underestimated by LR-TDDFT, and the error becomes smaller making the TDA. Neither SF1-TDDFT-TDA nor SF2-TDDFT-TDA provides a lower mean unsigned error than LR-TDDFT or TDDFT-TDA. The comparison between collinear and noncollinear kernels shows that the noncollinear kernel drastically reduces the spin contamination in the systems considered here, and it makes the results more accurate than collinear spin-flip TDDFT for functionals with a low percentage of Hartree-Fock exchange and sometimes for functionals with a higher percentage of Hartree-Fock exchange, but it yields less accurate results than ground-state TDDFT. (C) 2013 American Institute of Physics. [http://dx.doi.org/10.1063/1.4798402]. |
| 9. |
Miho Isegawa, Satoshi Maeda, Dean J. Tantillo, Keiji Morokuma, Predicting pathways for terpene formation from first principles - routes to known and new sesquiterpenes, CHEMICAL SCIENCE, 2014.02, Application of the Artificial Force Induced Reaction (AFIR) method to the prediction of cyclization/rearrangement pathways for carbocation precursors to sesquiterpenes is described. This method captures many of the features revealed in previous studies as well as new ones, including a pathway to a sesquiterpene not yet isolated in nature that we suspect will be isolated in time.. |
| 10. |
Miho Isegawa, Fengyi Liu, Satoshi Maeda, Keiji Morokuma, Ab initio reaction pathways for photodissociation and isomerization of nitromethane on four singlet potential energy surfaces with three roaming paths, JOURNAL OF CHEMICAL PHYSICS, 10.1063/1.4883916, 140, 24, 2014.06, Photodissociation pathways of nitromethane following pi -> pi* electronic excitation are reported. The potential energy surfaces for four lowest singlet states are explored, and structures of many intermediates, dissociation limits, transition states, and minimum energy conical intersections were determined using the automated searching algorism called the global reaction route mapping strategy. Geometries are finally optimized at CASSCF(14e, 11o) level and energies are computed at CAS(14o, 11e) PT2 level. The calculated preferable pathways and important products qualitatively explain experimental observations. The major photodissociation product CH3 and NO2 (B-2(2)) is formed by direct dissociation from the S-1 state. Important pathways involving S-1 and S-0 states for production of various dissociation products CH3NO + O (D-1), CH3O((XE)-E-2) + NO (X-2 Pi), CH2NO + OH, and CH2O + HNO, as well as various isomerization pathways have been identified. Three roaming processes also have been identified: the O atom roaming in O dissociation from CH3NO2, the OH radical roaming in OH dissociation from CH2N(O)(OH), and the NO roaming in NO dissociation from CH3ONO. (C) 2014 AIP Publishing LLC.. |
| 11. |
Bo Wang, Ke R. Yang, Xuefei Xu, Miho Isegawa, Hannah R. Leverentz, Donald G. Truhlar, Quantum Mechanical Fragment Methods Based on Partitioning Atoms or Partitioning Coordinates, ACCOUNTS OF CHEMICAL RESEARCH, 10.1021/ar500068a, 47, 9, 2731-2738, 2014.09, CONSPECTUS: The development of more efficient and more accurate ways to represent reactive potential energy surfaces is a requirement for extending the simulation of large systems to more complex systems, longer-time dynamical processes, and more complete statistical mechanical sampling. One way to treat large systems is by direct dynamics fragment methods. Another way is by fitting system-specific analytic potential energy functions with methods adapted to large systems. Here we consider both approaches.First we consider three fragment methods that allow a given monomer to appear in more than one fragment. The first two approaches are the electrostatically embedded many-body (EE-MB) expansion and the electrostatically embedded many-body expansion of the correlation energy (EE-MB-CE), which we have shown to yield quite accurate results even when one restricts the calculations to include only electrostatically embedded dimers. The third fragment method is the electrostatically embedded molecular tailoring approach (EE-MTA), which is more flexible than EE-MB and EE-MB-CE. We show that electrostatic embedding greatly improves the accuracy of these approaches compared with the original unembedded approaches.Quantum mechanical fragment methods share with combined quantum mechanical/molecular mechanical (QM/MM) methods the need to treat a quantum mechanical fragment in the presence of the rest of the system, which is especially challenging for those parts of the rest of the system that are close to the boundary of the quantum mechanical fragment. This is a delicate matter even for fragments that are not covalently bonded to the rest of the system, but it becomes even more difficult when the boundary of the quantum mechanical fragment cuts a bond. We have developed a suite of methods for more realistically treating interactions across such boundaries. These methods include redistributing and balancing the external partial atomic charges and the use of tuned fluorine atoms for capping dangling bonds, and we have shown that they can greatly improve the accuracy.Finally we present a new approach that goes beyond QM/MM by combining the convenience of molecular mechanics with the accuracy of fitting a potential function to electronic structure calculations on a specific system. To make the latter practical for systems with a large number of degrees of freedom, we developed a method to interpolate between local internal-coordinate fits to the potential energy. A key issue for the application to large systems is that rather than assigning the atoms or monomers to fragments, we assign the internal coordinates to reaction, secondary, and tertiary sets. Thus, we make a partition in coordinate space rather than atom space. Fits to the local dependence of the potential energy on tertiary coordinates are arrayed along a preselected reaction coordinate at a sequence of geometries called anchor points; the potential energy function is called an anchor points reactive potential.Electrostatically embedded fragment methods and the anchor points reactive potential, because they are based on treating an entire system by quantum mechanical electronic structure methods but are affordable for large and complex systems, have the potential to open new areas for accurate simulations where combined QM/MM methods are inadequate.. |
| 12. |
Miho Isegawa, Fengyi Liu, Satoshi Maeda, Keiji Morokuma, Complete active space second order perturbation theory (CASPT2) study of N(D-2) + H2O reaction paths on D-1 and D-0 potential energy surfaces: Direct and roaming pathways, JOURNAL OF CHEMICAL PHYSICS, 10.1063/1.4897633, 141, 15, 2014.10, We report reaction paths starting from N(D-2) + H2O for doublet spin states, D-0 and D-1. The potential energy surfaces are explored in an automated fashion using the global reaction route mapping strategy. The critical points and reaction paths have been fully optimized at the complete active space second order perturbation theory level taking all valence electrons in the active space. In addition to direct dissociation pathways that would be dominant, three roaming processes, two roaming dissociation, and one roaming isomerization: (1) H2ON -> H-O(H)N -> H-HON -> NO((2)Pi) + H-2, (2) cis-HNOH. HNO-H -> H-HNO -> NO + H-2, (3) H2NO -> H-HNO -> HNO-H -> trans-HNOH, are confirmed on the D-0 surface. (C) 2014 AIP Publishing LLC.. |
| 13. |
Miho Isegawa, Keiji Morokuma, Photochemical Ring Opening and Closing of Three Isomers of Diarylethene: Spin-Flip Time-Dependent Density Functional Study, JOURNAL OF PHYSICAL CHEMISTRY A, 10.1021/jp511474f, 119, 18, 4191-4199, 2015.05, The reaction mechanism of photochemical ring opening and closing transformation was investigated for diarylethene (DAE), which works as a molecular switch and photodevice. Spin-flip time-dependent density functional theory is employed to map the potential energy surfaces and to elucidate the photochemical mechanism of three isomers (normal, inverse, and mixed types) of 1,2-dithienylethene, a model DAE. The potential energy characteristics including the minimum-energy conical intersection reveals the origin of different product preferences of the three isomers. For the normal type, the excited state from either closed or open form reaches the same conical intersection that gives preferentially the closed product. The inverse type preferentially gives the closed product. The mixed type has two pathways that are easily convertible, and both open and closed reactants give both open and closed products.. |
| 14. |
Miho Isegawa, Frank Neese, Dimitrios A. Pantazis, Ionization Energies and Aqueous Redox Potentials of Organic Molecules: Comparison of DFT, Correlated ab Initio Theory and Pair Natural Orbital Approaches, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10.1021/acs.jctc.6b00252, 12, 5, 2272-2284, 2016.05, The calculation of redox potentials involves large energetic terms arising from gas phase ionization energies, thermodynamic contributions, and solvation energies of the reduced and oxidized species. In this work we study the performance of a wide range of wave function and density functional theory methods for the prediction of ionization energies and aqueous one-electron oxidation potentials of a set of 19 organic molecules. Emphasis is placed on evaluating methods that employ the computationally efficient local pair natural orbital (LPNO) approach, as well as several implementations of coupled cluster theory and explicitly correlated F12 methods. The electronic energies are combined with implicit solvation models for the solvation energies. With the exception of MP2 and its variants, which suffer from enormous errors arising at least partially from the poor Hartree Fock reference, ionization energies can be systematically predicted with average errors below 0.1 eV for most of the correlated wave function based methods studies here, provided basis set extrapolation is performed. LPNO methods are the most efficient way to achieve this type of accuracy. DFT methods show in general larger errors and suffer from inconsistent behavior. The only exception is the M06-2X functional which is found to be competitive with the best LPNO-based approaches for ionization energies. Importantly, the limiting factor for the calculation of accurate redox potentials is the solvation energy. The errors in the predicted solvation energies by all continuum solvation models tested in this work dominate the final computed reduction potential, resulting in average errors typically in excess of 0.3 V and hence obscuring the gains that arise from choosing a more accurate electronic structure method.. |
| 15. |
Miho Isegawa, W. M. C. Sameera, Akhilesh K. Sharma, Taku Kitanosono, Masako Kato, Shu Kobayashi, Keiji Morokuma, Copper-Catalyzed Enantioselective Boron Conjugate Addition: DFT and AFIR Study on Different Selectivities of Cu(I) and Cu(II) Catalysts, ACS CATALYSIS, 10.1021/acscatal.7b01152, 7, 8, 5370-5380, 2017.08, We present a mechanistic survey on the LCu-catalyzed (L = chiral 2,2'-bipyridine ligand) enantioselective boron conjugate addition reaction, carried out using density functional theory (DFT) and artificial force induced reaction (AFIR) methods. The computed catalytic cycle for Cu(I)- and Cu(II)-based catalysts consists of three steps: (a) boron boron bond cleavage of B-2(pin)(2), (b) boron conjugate addition on the beta carbon of chalcone, and (c) protonation. The enantioselectivity of the reaction with LCuI or LCuII catalysts is solely governed at the boron conjugate addition step. The multicomponent(MC)-AFIR search and the subsequent DFT calculations for the LCuI catalyst determined transition states (TSs), which lead to Cu-I-O-enolate and Cu-I-C-enolate, and both equally contribute to the C-B bond formation with no enantioselectivity. On the other hand, a MC-AFIR search and the subsequent DFT calculations for the analogous LCuII catalyst showed that only the transition state (TS) leading to Cu-II-O-enolate contributes to the reaction. Furthermore, the TSs leading to the R and S forms of Cu-II-O-enolates are energetically well separated, with the R form being of lower energy, which is consistent with experimental observations. Our study provides important mechanistic insights for designing transition-metal catalysts for Cu-catalyzed enantioselective boron conjugate addition reactions.. |
| 16. |
Miho Isegawa, Akhilesh K. Sharma, Seiji Ogo, Keiji Morokuma, DFT Study on Fe(IV)-Peroxo Formation and H Atom Transfer Triggered O-2 Activation by NiFe Complex, ORGANOMETALLICS, 10.1021/acs.organomet.8b00098, 37, 10, 1534-1545, 2018.05, The mechanism for dioxygen activation using the biomimetic model complex of [NiFe]-hydrogenase, [NiLFe(eta(5)-C5Me5 )](+) [L = N,N'-diethyl-3,7-diazanonane-1,9-dithiolato] was established using density functional theory (DFT) and artificial force-induced reaction (AFIR) methods. Our computational results suggest that O-2 binds to the Fe-II center in an end-on fashion and forms a high-valent iron complex, ((NiFeIV)-Fe-II(eta(2)-O-2) NiFe-peroxo O-2)), which has been experimentally observed. The O-O bond cleavage occurs in the presence of borohydride (BH4-) through hydrogen atom transfer (HAT). Once the HAT occurs, the generated BH 3 radical anion (BH3 center dot-) binds to the terminal oxygen of NiFe-OOH, giving rise to BH3OH- and (NiFeIV)-Fe-II=O. The second HAT from BH4- to the oxygen of (NiFeIV)-Fe-II=O leads to BH3OH- and Fe-reduced complex. Importantly, the dioxygen activation is triggered by HAT, not by proton transfer or hydride transfer. The O-2 is activated by the Fe center, and the oxidation state of Fe varies during the process, while the oxidation state of Ni is conserved. These mechanistic insights into O-2 activation are essential in understanding the formation of the inactive state and reactivation process in hydrogenase.. |
| 17. |
Miho Isegawa, Akhilesh K. Sharma, Seiji Ogo, Keiji Morokuma, Electron and Hydride Transfer in a Redox-Active NiFe Hydride Complex: A DFT Study, ACS CATALYSIS, 10.1021/acscatal.8b02368, 8, 11, 10419-10429, 2018.11, We present mechanistic details of the formation of a NiFe hydride complex and provide information on its electron-and hydride-transfer processes on the basis of density functional theory calculations and artificial-force induced-reaction studies. The NiFe hydride complex conducts three transfer reactions: namely, electron transfer, hydride transfer, and proton transfer. In a NiFe hydride complex, the hydride binds to Fe, which is different from the Ni-R state in hydrogenase where the hydride is located between Ni and Fe. According to our calculations, in reaction with the ferrocenium ion, electron transfer occurs from the NiFe hydride complex to the ferrocenium ion, followed by a hydrogen atom transfer (HAT) to the second ferrocenium ion. The oxidation state of Fe varies during the redox process, different from the case of NiFe hydrogenase, where the oxidation state of Ni varies. A single-step hydride transfer occurs in the presence of a 10-methylacridinium ion (AcrH(+)), which is more kinetically feasible than the HAT process. In contrast to the HAT and hydride-transfer process, the proton transfer occurs through a low barrier from a protonated diethyl ether. The revealed reaction mechanism guides the interpretation of the catalytic cycle of NiFe hydrogenase and leads to the development of efficient biomimetic catalysts for H-2 generation and an electron/hydride transfer.. |
| 18. |
Miho Isegawa, Akhilesh K. Sharma, CO2 reduction by a Mn electrocatalyst in the presence of a Lewis acid: a DFT study on the reaction mechanism, SUSTAINABLE ENERGY & FUELS, 10.1039/c9se00213h, 3, 7, 1730-1738, 2019.07, The addition of a Lewis acid (Mg2+) has been shown to improve the efficiency of CO2 reduction by homogeneous electrocatalysts. Recently, a CO2 reduction protocol involving a Mn electrocatalyst with a bulky bipyridine ligand [Mn(mesbpy)(CO)(3) MeCN](mesbpy = 6,6 '-dimesityl-2,2 '-bipyridine) in the presence of Mg(OTf)(2) was reported (Sampson et al., J. Am. Chem. Soc., 2016, 138, 1386-1393). However, a detailed mechanistic understanding of this reaction is lacking. Here we present the details of the reaction mechanism based on thermodynamic and kinetic data derived from density functional theory (DFT) calculations. The DFT calculations demonstrate that the primary role of Mg(OTf)(2) is to stabilize a two-electron reduced Mn intermediate through Lewis pair binding. Furthermore, Mg(OTf)(2) makes the reaction thermodynamically and kinetically feasible. In our presented mechanism, two molecules of CO2 and Mg(OTf)(2) contribute to the C-O bond cleavage reaction. The demonstrated roles of Mg(OTf)(2) in this catalytic process are important for the design of novel multimetallic catalysts for CO2 conversion under milder reaction conditions.. |
| 19. |
Miho Isegawa, Takahiro Matsumoto, Seiji Ogo, Selective Oxidation of H-2 and CO by Nilr Catalyst in Aqueous Solution: A DFT Mechanistic Study, INORGANIC CHEMISTRY, 10.1021/acs.inorgchern.9b02400, 59, 2, 1014-1028, 2020.01, One of the challenges in utilizing hydrogen gas (H-2) as a sustainable fossil fuel alternative is the inhibition of H-2 oxidation by carbon monoxide (CO), which is involved in the industrial production of H-2 sources. To solve this problem, a catalyst that selectively oxidizes either CO or H-2 or one that co-oxidizes H-2 and CO is needed. Recently, a NiIr catalyst [(NiCl)-Cl-II(X)(IrCl)-Cl-III(eta(5)-C5Me5)], (X = N,N'-dimethyl-3,7-diazanonane-1,9-dithiolate), which efficiently and selectively oxidizes either H-2 or CO depending on the pH, has been developed (Angew. Chem. Int. Ed. 2017, 56, 9723-9726). In the present work, density functional theory (DFT) calculations are employed to elucidate the pH-dependent reaction mechanisms of H-2 and CO oxidation catalyzed by this NiIr catalyst. During H-2 oxidation, our calculations suggest that dihydrogen binds to the Ir center and generates an Ir(III)-dihydrogen complex, followed by subsequent isomerization to an Ir(V)-dihydride species. Then, a proton is abstracted by a buffer base, CH3COO-, resulting in the formation of a hydride complex. The catalytic cycle completes with electron transfer from the hydride complex to a protonated 2,6-dichlorobenzeneindophenol (DCIP) and a proton transfer from the oxidized hydride complex to a buffer base. The CO oxidation mechanism involves three distinct steps, i.e., (1) formation of a metal carbonyl complex, (2) formation of a metallocarboxylic acid, and (3) conversion of the metallocarboxylic acid to a hydride complex. The formation of the metallocarboxylic acid involves nucleophilic attack of OH- to the carbonyl-C followed by a large structural change with concomitant cleavage of the Ir-S bond and rotation of the COOH group along the NiIr axis. During the conversion of the metallocarboxylic acid to the hydride complex, intramolecular proton transfer followed by removal of CO2 leads to the formation of the hydride complexes. In addition, the barrier heights for the binding of small molecules (H-2, OH-, H2O, and CO) to Ir were calculated, and the results indicated that dissociation from Ir is a faster process than the binding of H2O and H-2. These calculations indicate that H-2 oxidation is inhibited by CO and OH- and thus prefers acidic conditions. In contrast, the CO oxidation reactions occur more favorably under basic conditions, as the formation of the metallocarboxylic acid involves OH- attack to a carbonyl-C and the binding of OH- to Ni largely stabilizes the triplet spin state of the complex. Taken together, these calculations provide a rationale for the experimentally observed pH-dependent, selective oxidations of H-2 and CO.. |
| 20. |
Seiji Ogo, Takahiro Kishima, Takeshi Yatabe, Keishi Miyazawa, Ryunosuke Yamasaki, Takahiro Matsumoto, Tatsuya Ando, Mitsuhiro Kikkawa, Miho Isegawa, Ki-Seok Yoon, Shinya Hayami, [NiFe], [FeFe], and [Fe] hydrogenase models from isomers., Science advances, 10.1126/sciadv.aaz8181, 6, 24, eaaz8181, 2020.06, The study of hydrogenase enzymes (H2ases) is necessary because of their importance to a future hydrogen energy economy. These enzymes come in three distinct classes: [NiFe] H2ases, which have a propensity toward H2 oxidation; [FeFe] H2ases, which have a propensity toward H2 evolution; and [Fe] H2ases, which catalyze H- transfer. Modeling these enzymes has so far treated them as different species, which is understandable given the different cores and ligand sets of the natural molecules. Here, we demonstrate, using x-ray analysis and nuclear magnetic resonance, infrared, Mössbauer spectroscopies, and electrochemical measurement, that the catalytic properties of all three enzymes can be mimicked with only three isomers of the same NiFe complex.. |
