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1.
Dalton Trans ; 53(15): 6556-6567, 2024 Apr 16.
Article in English | MEDLINE | ID: mdl-38525694

ABSTRACT

The µ-nitrido-bridged iron phthalocyanine homodimer is a potent molecule-based CH4 oxidation catalyst that can effectively oxidize chemically stable CH4 under mild reaction conditions in an acidic aqueous solution including an oxidant such as H2O2. The reactive intermediate is a high-valent iron-oxo species generated upon reaction with H2O2. However, a detailed comparison of the CH4 oxidation activity of the µ-nitrido-bridged iron phthalocyanine dimer with those of µ-nitrido-bridged iron porphyrinoid dimers containing one or two porphyrin ring(s) has not been yet reported, although porphyrins are the most important class of porphyrinoids. Herein, we compare the catalytic CH4 and CH3CH3 oxidation activities of a monocationic µ-nitrido-bridged iron porphyrin homodimer and a monocationic µ-nitrido-bridged heterodimer of an iron porphyrin and an iron phthalocyanine with those of a monocationic µ-nitrido-bridged iron phthalocyanine homodimer in an acidic aqueous solution containing H2O2 as an oxidant. It was demonstrated that the CH4 oxidation activities of monocationic µ-nitrido-bridged iron porphyrinoid dimers containing porphyrin ring(s) were much lower than that of a monocationic µ-nitrido-bridged iron phthalocyanine homodimer. These findings suggested that the difference in the electronic structure of the porphyrinoid rings of monocationic µ-nitrido-bridged iron porphyrinoid dimers strongly affected their catalytic light alkane oxidation activities.

2.
J Am Chem Soc ; 146(13): 9311-9317, 2024 Apr 03.
Article in English | MEDLINE | ID: mdl-38502926

ABSTRACT

A π-conjugated molecule with one electronic spin often forms a π-stacked dimer through molecular orbital interactions between two unpaired electrons. The bonding is recognized as a multicentered two-electron interaction between the two π-conjugated molecules. Here, we disclose a multicentered bonding interaction between two antiaromatic molecules involving four electrons. We have synthesized an antiaromatic porphyrin analogue, Ni(II) bis(pentafluorophenyl)norcorrole. Its dimer adopts a face-to-face stacked structure with an extremely short stacking distance of 2.97 Å. The close stacking originates from a multicenter four-electron bonding interaction between the two molecules. The bonding electrons were experimentally observed via synchrotron X-ray diffraction analysis and corroborated by theoretical calculations. The intermolecular interaction of the molecular orbitals imparts the stacked dimer with aromatic character that is distinctly different from that of its monomer.

3.
Phys Chem Chem Phys ; 26(14): 10711-10722, 2024 Apr 03.
Article in English | MEDLINE | ID: mdl-38512217

ABSTRACT

Developing innovative platinum-based electrocatalysts and enhancing their efficiency are crucial for advancing high-performance fuel cell technology. In this study, we employed DFT calculations to provide a theoretical basis for interpreting the impact of graphene coatings on various Pt surfaces on oxygen reduction reaction (ORR) catalytic activity, which are currently applied as protective layers in experiments. We comprehensively assess the geometric and electronic properties of Pt(100), Pt(110), and Pt(111) surfaces in comparison to their graphene-coated counterparts, revealing different adsorption behaviors of O2 across these surfaces. The ORR mechanisms on different Pt surfaces show distinct rate-determining steps, with Pt(111) showing the highest ORR activity, followed by Pt(110) and Pt(100). Graphene coatings play a key role in enhancing charge transfer from the surface, resulting in modifications of O2 adsorption. Despite influencing ORR kinetics, these graphene-coated surfaces demonstrate competitive catalytic activity compared to their bare counterparts. Notably, Pt(111) with a graphene coating exhibits the lowest activation energy among graphene-coated surfaces. Our calculations also suggest that the ORR can occur directly on non-defective Pt@graphene surfaces rather than being restricted to exposed Pt centers due to point defects on graphene. Furthermore, our work highlights the potential of nitrogen doping onto the Pt(111)@C surface to further enhance ORR activity. This finding positions nitrogen-doped Pt@C as a promising electrocatalyst for advancing electrochemical technologies.

4.
Angew Chem Int Ed Engl ; 63(15): e202400711, 2024 Apr 08.
Article in English | MEDLINE | ID: mdl-38315771

ABSTRACT

The development of near-infrared (NIR) fluorophores that have both excellent chemical stability and photostability, as well as efficient cell permeability, is highly demanded. In this study, we present phospha-rhodamine (POR) dyes which display significantly improved performance for protein labeling. This is achieved by incorporating a 2-carboxy-3-benzothiophenyl group at the 9-position of the xanthene scaffold. The resulting cis and trans isomers were successfully isolated and structurally characterized using X-ray diffraction. The HaloTag ligand conjugates of the two isomers exhibited different staining abilities in live cells. While the cis isomer showed non-specific accumulation on the organelle membranes, the trans isomer selectively labeled the HaloTag-fused proteins, enabling the long-term imaging of cell division and the 5-color imaging of cell organelles. Molecular dynamics simulations of the HaloTag ligand conjugates within the lipid membrane suggested that the cis isomer is more prone to forming oligomers in the membrane. In contrast, the oligomerization of the trans isomer is effectively suppressed by its interaction with the lipid molecules. By taking advantage of the superior labeling performance of the trans isomer and its NIR-emissive properties, multi-color time-lapse super-resolution 3D imaging, namely super-resolution 5D-imaging, of the interconnected network between the endoplasmic reticulum and microtubules was achieved in living cells.


Subject(s)
Fluorescent Dyes , Organelles , Rhodamines , Ligands , Fluorescent Dyes/chemistry , Organelles/metabolism , Proteins , Microscopy, Fluorescence/methods , Lipids
5.
Inorg Chem ; 62(49): 20496-20505, 2023 Dec 11.
Article in English | MEDLINE | ID: mdl-38010736

ABSTRACT

A first DMRG/CASSCF-CASPT2 study of a series of paradigmatic {FeNO}6, {FeNO}7, and {FeNO}8 heme-nitrosyl complexes has led to substantial new insight as well as uncovered key shortcomings of the DFT approach. By virtue of its balanced treatment of static and dynamic correlation, the calculations have provided some of the most authoritative information available to date on the energetics of low- versus high-spin states of different classes of heme-nitrosyl complexes. Thus, the calculations indicate low doublet-quartet gaps of 1-4 kcal/mol for {FeNO}7 complexes and high singlet-triplet gaps of ≳20 kcal/mol for both {FeNO}6 and {FeNO}8 complexes. In contrast, DFT calculations yield widely divergent spin state gaps as a function of the exchange-correlation functional. DMRG-CASSCF calculations also help calibrate DFT spin densities for {FeNO}7 complexes, pointing to those obtained from classic pure functionals as the most accurate. The general picture appears to be that nearly all the spin density of Fe[P](NO) is localized on the Fe, while the axial ligand imidazole (ImH) in Fe[P](NO)(ImH) pushes a part of the spin density onto the NO moiety. An analysis of the DMRG-CASSCF wave function in terms of localized orbitals and of the resulting configuration state functions in terms of resonance forms with varying NO(π*) occupancies has allowed us to address the longstanding question of local oxidation states in heme-nitrosyl complexes. The analysis indicates NO(neutral) resonance forms [i.e., Fe(II)-NO0 and Fe(III)-NO0] as the major contributors to both {FeNO}6 and {FeNO}7 complexes. This finding is at variance with the common formulation of {FeNO}6 hemes as Fe(II)-NO+ species but is consonant with an Fe L-edge XAS analysis by Solomon and co-workers. For the {FeNO}8 complex {Fe[P](NO)}-, our analysis suggests a resonance hybrid description: Fe(I)-NO0 ↔ Fe(II)-NO-, in agreement with earlier DFT studies. Vibrational analyses of the compounds studied indicate an imperfect but fair correlation between the NO stretching frequency and NO(π*) occupancy, highlighting the usefulness of vibrational data as a preliminary indicator of the NO oxidation state.

6.
ACS Appl Mater Interfaces ; 15(37): 43871-43879, 2023 Sep 20.
Article in English | MEDLINE | ID: mdl-37676926

ABSTRACT

The development of flexible thermoelectric devices requires materials possessing ductility and high thermoelectric performance at room temperature. However, only a few existing materials meet both criteria. In this study, the ductile properties, electronic structure, and transport properties of the low-temperature phase α-AgCuS were elucidated using first-principles calculations combined with Boltzmann transport theory. With a layered zigzag structure similar to the well-known ductile semiconductor Ag2S, AgCuS is determined to have good metal-like ductility. Through consideration of various intrinsic scattering mechanisms, we found that electron-polar optical phonon interactions have the most significant impact on the transport behavior of AgCuS. The predominance of this type of interaction is also disclosed by the covalent-ionic bonding nature of the Ag-S and Cu-S bonds. Therefore, weakening this interaction via doping or alloying could optimize the thermoelectric performance of the system. At room temperature, a maximum dimensionless figure of merit ZT of up to 0.592 could be achieved under a tuning of hole concentration to 2 × 1019 cm-3, suggesting that α-AgCuS could be a promising p-type candidate for flexible thermoelectric applications.

7.
J Phys Chem A ; 127(36): 7544-7556, 2023 Sep 14.
Article in English | MEDLINE | ID: mdl-37651105

ABSTRACT

A systematic analysis was conducted to explore the spin-state energetics of a series of 19 FeN4 complexes. The performance of a large number of multireference methods was assessed, highlighting the significant challenges associated with accurately describing the spin-state energetics of FeN4 complexes. Most multireference methods were found to be susceptible to errors originating from the reference CASSCF wavefunction, leading to an overstabilization of high-spin states. Nonetheless, a few multireference methods, namely, CASPT2/CC, DSRG-MRPT3, and LDSRG(2), demonstrated promising performance compared to the benchmark CCSD(T) method. Furthermore, our study revealed that FeN4 complexes having a quintet ground state are exceedingly rare. Accordingly, only one specific model (Fe(L2)) and one synthesized complex (Fe(OTBP)) have the quintet ground state among the studied complexes. This scarcity of quintet FeN4 complexes highlights the unique nature of these systems and raises intriguing questions regarding the factors influencing spin states, such as the size of the macrocycle cavity, the introduction of substituents, or the induction of out-of-plane deformation.

8.
J Phys Chem A ; 125(17): 3579-3588, 2021 May 06.
Article in English | MEDLINE | ID: mdl-33904746

ABSTRACT

The alkaline earth metal trimer cluster dianions Be32- and Mg32- lie energetically above their respective monoanions and can therefore decay by electron autodetachment. Consequently, these dianions possess only short-lived resonance states, and here we study these states using regularized analytic continuation as well as complex absorbing potentials combined with a wide a variety of quantum chemistry methods including CCSD(T), SACCI, EOM-CCSD, CASPT2, and NEVPT2. For both Be32- and Mg32-, four low-energy resonance states corresponding to different occupation patterns of the two excess electrons in the two lowest p-σ and p-π orbitals are identified: Two states are dominated by doubly occupied configurations and can be characterized as showing σ and π aromatic character. The other two states correspond to the open-shell singlet/triplet pair. All dianion states are found to be highly unstable and to possess short lifetimes: They show resonance positions in the energy range 2.3-4.3 eV above the ground states of their respective monoanions and broad widths between 1 and 1.5 eV translating into femtosecond lifetimes. For both Be32- and Mg32-, the differences between the four states are small, but the triplet states tend to be slightly more stable than the three singlet states. Thus, in the case of the multicharged ion aromatic character of the excess electrons takes second stage while Coulomb repulsion takes front and center. In addition to the two isolated cluster dianions, model stabilization by small water clusters is explored. Our results show a dramatic drop in resonance position and width corresponding to a lifetime increase by 2 orders of magnitude. However, the "solvated" clusters are still resonances, and a more pronounced perturbation by, for example, yet larger water clusters or a ligand environment providing larger bond dipoles will be needed to fully stabilize two excess electrons localized on a small system such as an alkaline metal trimer.

9.
JACS Au ; 1(12): 2303-2314, 2021 Dec 27.
Article in English | MEDLINE | ID: mdl-34984418

ABSTRACT

Hybrid density functional theory (B3LYP) and density matrix renormalization group (DMRG) theory have been used to quantitatively compare the degree of ligand noninnocence (corrole radical character) in seven archetypal metallocorroles. The seven complexes, in decreasing order of corrole noninnocent character, are Mn[Cor]Cl > Fe[Cor]Cl > Fe[Cor](NO) > Mo[Cor]Cl2 > Ru[Cor](NO) ≈ Mn[Cor]Ph ≈ Fe[Cor]Ph ≈ 0, where [Cor] refers to the unsubstituted corrolato ligand. DMRG-based second-order perturbation theory calculations have also yielded detailed excited-state energetics data on the compounds, shedding light on periodic trends involving middle transition elements. Thus, whereas the ground state of Fe[Cor](NO) (S = 0) is best described as a locally S = 1/2 {FeNO}7 unit antiferromagnetically coupled to a corrole A' radical, the calculations confirm that Ru[Cor](NO) may be described as simply {RuNO}6-Cor3-, that is, having an innocent corrole macrocycle. Furthermore, whereas the ferromagnetically coupled S = 1{FeNO}7-Cor•2- state of Fe[Cor](NO) is only ∼17.5 kcal/mol higher than the S = 0 ground state, the analogous triplet state of Ru[Cor](NO) is higher by a far larger margin (37.4 kcal/mol) relative to the ground state. In the same vein, Mo[Cor]Cl2 exhibits an adiabatic doublet-quartet gap of 36.1 kcal/mol. The large energy gaps associated with metal-ligand spin coupling in Ru[Cor](NO) and Mo[Cor]Cl2 reflect the much greater covalent character of 4d-π interactions relative to analogous interactions involving 3d orbitals. As far as excited-state energetics is concerned, DMRG-CASPT2 calculations provide moderate validation for hybrid density functional theory (B3LYP) for qualitative purposes, but underscore the possibility of large errors (>10 kcal/mol) in interstate energy differences.

10.
Phys Chem Chem Phys ; 22(46): 27037-27052, 2020 Dec 07.
Article in English | MEDLINE | ID: mdl-33215620

ABSTRACT

A recently introduced framework incorporating the Projector Augmented Wave method and Gauss-type function (GTF-PAW) [X.-G. Xiong and T. Yanai, J. Chem. Theory Comput., 2017, 13, 3236-3249] opens alternative possibilities for performing low-cost molecular computational chemistry calculations. In this work, we present our first attempt to expand the applicability of this method by developing a family of compact general contracted polarization consistent basis sets (PAW-Ln) as an optimized GTF basis in combination with PAW. The results show that PAW-Ln, despite having small numbers of primitives, can provide not only better performance than effective core potential (ECP) but also good accuracy and desirable systematic convergence compared to larger all-electron basis sets. This demonstrates that GTF-PAW using the PAW-Ln basis sets could be a better alternative to both conventional all-electron- and ECP-based approaches for routine DFT calculations.

11.
Inorg Chem ; 59(16): 11493-11502, 2020 Aug 17.
Article in English | MEDLINE | ID: mdl-32799474

ABSTRACT

An elaborate study with multireference second-order perturbation theory has been performed to elucidate the electronic structure and relative energy of three relevant states of FeNO corroles, namely the S = 0 ground state, the lowest S = 1 state, and the anion S = 1/2 state. On the basis of CASSCF and DMRG calculations with an active space including up to 37 orbitals, the electronic structure of the ground state was analyzed, with special emphasis on the diradical nature of the Fe-corrole and Fe-NO bonds. The results essentially confirm an earlier suggestion from B3LYP of a non-innocent corrole•2- bound to an {FeNO}7 unit, although the contribution of diradical character to the iron-corrole bond is found to be limited to 35%. This limited diradical character explains the high relative energy (16.5 kcal/mol) of the corresponding triplet state, where the corrole•2- is ferromagnetically coupled to the S = 1/2 {FeNO}7 unit. Consistent with experimental findings, reduction is found to take place at the corrole ligand, with a calculated electron affinity of 52.5 kcal/mol. The results obtained from the correlated calculations were also compared to DFT with a broad range of functionals.

12.
J Chem Theory Comput ; 16(4): 2606-2616, 2020 Apr 14.
Article in English | MEDLINE | ID: mdl-32105477

ABSTRACT

Electronic resonances are metastable (N + 1) electron states, in other words, discrete states embedded in an electronic continuum. While great progress has been made for certain types of resonances-for example, temporary anions created by attaching one excess electron to a closed shell neutral-resonances in general remain a great challenge of quantum chemistry because a successful description of the decay requires a balanced description of the bound and continuum aspect of the resonance. Here, a smoothed Voronoi complex absorbing potential (CAP) is combined with the XMS-CASPT2 method, which enables us to address the balance challenge by appropriate choice of the CAS space. To reduce the computational cost, the method is implemented in the projected scheme. In this pilot application, three temporary anions serve as benchmarks: the π* resonance state of formaldehyde; the π* and σ* resonance states of chloroethene as functions of the C-Cl bond dissociation coordinate; and the 4Πu and 2Πu resonance states of N2-. The convergence of the CAP/XMS-CASPT2 results has been systematically examined with respect to the size of the active space. Resonance parameters predicted by the CAP/XMS-CASPT2 method agree well with CAP/SAC-CI results (deviations of about 0.15 eV); however, as expected, CAP/XMS-CASPT2 has clear advantages in the bond dissociation region. The advantages of CAP/XMS-CASPT2 are further demonstrated in the calculations of 4Πu and 2Πu resonance states of N2- including their 3Σu+ and 3Δu parent states. Three of the involved states (2Πu, 3Σu+, and 3Δu) possess multireference character, and CAP/XMS-CASPT2 can easily describe these states with a relatively modest active space.

13.
J Chem Theory Comput ; 15(11): 5925-5964, 2019 Nov 12.
Article in English | MEDLINE | ID: mdl-31509407

ABSTRACT

In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics, and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the Article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism, and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with postcalculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory, and new electronic and muonic basis sets.

14.
J Chem Theory Comput ; 15(8): 4297-4304, 2019 Aug 13.
Article in English | MEDLINE | ID: mdl-31265281

ABSTRACT

We employed our recently proposed multireference approach CASPT2/CC to calculate the quintet-triplet gaps ΔETQ of a series of non-heme FeIV═O species and subsequently used these results to benchmark density functional theory (DFT) as well as two variants of local coupled-cluster approaches (DLPNO-CCSD(T) and LUCCSD(T0)). We showed that current implementations of the local coupled-cluster method are not sufficiently accurate. DLPNO-CCSD(T) systematically overstabilizes the quintet state, whereas LUCCSD(T0) overestimates the triplet one. This sort of systematic bias may be helpful in improving local correlation methods and can also be used as the basis for a simple correction scheme.

15.
Chemistry ; 25(54): 12491-12496, 2019 Sep 25.
Article in English | MEDLINE | ID: mdl-31313861

ABSTRACT

Density functional theory (DFT) and an advanced ab initio technique based on density matrix renormalization group (DMRG-CASPT2) were employed to investigate a reactive N-bridged high-valent diiron-oxo species involved in H-abstraction reactions. We studied in detail two important doublet states, the ground state with two iron(IV) centers and a mixed valence FeV -FeIV excited state. We found that the latter state is low-lying. Furthermore, its electronic structure and spin density imply that it has significantly higher H-abstraction reactivity than the ground state. This low-lying excited state might be the reason behind the high oxidation reactivity of this diiron-oxo species towards methane.

16.
Inorg Chem ; 58(11): 7345-7356, 2019 Jun 03.
Article in English | MEDLINE | ID: mdl-31117625

ABSTRACT

The Mn-oxo porphyrin (MnOP) mechanism for substrate hydroxylation is computationally studied with the aim to better understand reactivity in these systems. Theoretical studies suggest Mn(V)OP species to be very reactive intermediates with thermally accessible reaction barriers represented by low-spin/high-spin-crossover occurring in the Mn(V)OP oxidant, and kinetics for selected Mn(V)OP species indeed find high reactivity. On the other hand, MnOP complexes lead to modest yields in hydroxylation reactions of several different substrates, implying low rate constants and high reaction barriers. The resolution of this inconsistency is very important to understand the reactivity of Mn-oxo porphyrins and to improve the catalytic conditions. In this work we use the toluene hydroxylation by the Mn(V)OP(H2O)+ complex as a case study to gain deep insight into the reaction mechanism. Minimum energy crossing point (MECP) results on the H-abstraction process from toluene indicate a first crossover from a singlet to a triplet spin state of the Mn(V)OP(H2O)+ species with a thermally accessible barrier, followed by a very facile H-abstraction by the triplet complex. Issues concerning (i) the validation of the level of the density functional theory employed (BP86) to describe the singlet-triplet energy gap in the Mn(V)OP(H2O)+ system versus highly accurate DMRG-CASPT2/CC calculations, and (ii) the influence of the axial ligand (X = none, Cl-, CH3CN, OH-, and O2-) on MnOP reactivity, which models the different experimental conditions, are addressed. The ligand trans influence mainly controls the reactivity through the singlet-triplet energy gap modulation, with the porphyrin ruffling distortion also finely tuning it. Finally, a stepwise model for the H-abstraction process is proposed which allows a direct comparison between the calculated and experimentally measured Gibbs free activation energy barriers ( Zhang et al. J. Am. Chem. Soc. 2005 , 127 , 6573 - 6582 ). The low yields in catalysis are shown not to be due to low reactivity of Mn(V).

17.
J Chem Theory Comput ; 15(5): 3033-3043, 2019 May 14.
Article in English | MEDLINE | ID: mdl-30995039

ABSTRACT

Employing second-order perturbation theory based on the density matrix renormalization group (DMRG-CASPT2), this work aims at providing a quantitative description of the spin state energetics of a chloro-ligated iron(IV)-oxo porphyrin as a model for the cytochromes P450 active species, also known as compound I (Cpd I). We explored DMRG-CASPT2 to its full extent with an extensive active space (up to 31 active orbitals) as well as a large number of renormalized states m (up to 10000). Different flavors of DMRG-CASPT2, using either the costly exact 4-particle reduced density matrix (4-RDM) or the cheaper cumulant approximated 4-RDM (cu(4)), were analyzed. All flavors essentially converge to similar relative energies between different spin states. Including a correction for the protein environment, we found a quartet FeIVO ground state and, more importantly, a thermally accessible doublet FeVO excited state that might directly contribute to the reactivity of this iron-oxo species. Our results also showed that cheaper approaches, such as CASPT2 based on a smaller active space or the cumulant approximation DMRG-cu(4)-CASPT2, are capable of accurately describing the spin state energetics of this species.

18.
J Chem Theory Comput ; 15(2): 922-937, 2019 Feb 12.
Article in English | MEDLINE | ID: mdl-30605326

ABSTRACT

In a large variety of studies, the coupled-cluster method with singles, doubles, and perturbative triples (CCSD(T)) is used as a reference for benchmarking the performance of density functional theory (DFT) functionals. In the case of open-shell species, this theory can be applied in different forms depending on the restricted or unrestricted treatment of spin. In this study, we show that these different approaches can produce results which deviate by ∼5 kcal/mol for different species on the potential energy surfaces. This was demonstrated for a simple model of the C-H activation carried out by non-heme iron enzymes. Assessing the limits of CCSD(T) prior to its use as a general benchmark tool is warranted. This was done using higher-order coupled-cluster calculations as well as multiconfigurational second-order perturbation theory (CASPT2), since iron-oxo species present some multireference character. Furthermore, we tested two different implementations of the local coupled-cluster method and compared them to the CCSD(T) results, showing that even though these novel approaches are promising, without further developments they appear not to be suitable for describing two-state reactivity of the system investigated in the current study. Additionally, we implemented and assessed the performance of the hotspot approach for the local unrestricted CCSD(T) scheme which aims at reducing the pair error for systems containing transition metals.

19.
Inorg Chem ; 57(24): 15289-15298, 2018 Dec 17.
Article in English | MEDLINE | ID: mdl-30500163

ABSTRACT

[NiFe] hydrogenases catalyze the reversible conversion of molecular hydrogen to protons and electrons. This seemingly simple reaction has attracted much attention because of the prospective use of H2 as a clean fuel. In this paper, we have studied the full reaction mechanism of this enzyme with various computational methods. Geometries were obtained with combined quantum mechanical and molecular mechanics (QM/MM) calculations. To get more accurate energies and obtain a detailed account of the surroundings, we performed big-QM calculations with 819 atoms in the QM region. Moreover, QM/MM thermodynamic cycle perturbation calculations were performed to obtain free energies. Finally, density matrix renormalisation group complete active space self-consistent field calculations were carried out to study the electronic structures of the various states in the reaction mechanism. Our calculations indicate that the Ni-L state is not involved in the reaction mechanism. Instead, the Ni-C state is reduced by one electron and then the bridging hydride ion is transferred to the sulfur atom of Cys546 as a proton and the two electrons transfer to the Ni ion. This step turned out to be rate-determining with an energy barrier of 58 kJ/mol, which is consistent with the experimental rate of 750 ± 90 s-1 (corresponding to ∼52 kJ/mol). The cleavage of the H-H bond is facile with an energy barrier of 33 kJ/mol, according to our calculations. We also find that the reaction energies are sensitive to the size of the QM system, the basis set, and the density functional theory method, in agreement with previous studies.


Subject(s)
Density Functional Theory , Hydrogenase/metabolism , Quantum Theory , Biocatalysis , Desulfovibrio vulgaris/enzymology , Electrons , Hydrogen/chemistry , Hydrogen/metabolism , Hydrogenase/chemistry , Models, Molecular , Molecular Structure , Protons
20.
Inorg Chem ; 57(23): 14603-14616, 2018 Dec 03.
Article in English | MEDLINE | ID: mdl-30418750

ABSTRACT

The iron(II) complexes of two structural isomers of 2-(1 H-imidazol-2-yl)diazine reveal how ligand design can be a successful strategy to control the electronic and magnetic properties of complexes by fine-tuning their ligand field. The two isomers only differ in the position of a single diazinic nitrogen atom, having either a pyrazine (Z) or a pyrimidine (M) moiety. However, [Fe(M)3](ClO4)2 is a spin-crossover complex with a spin transition at 241 K, whereas [Fe(Z)3](ClO4)2 has a stable magnetic behavior between 2 and 300 K. This is corroborated by temperature-dependent Mössbauer spectra showing the presence of a quintet and a singlet state in equilibrium. The temperature-dependent single-crystal X-ray diffraction results relate the spin-crossover observed in [Fe(M)3](ClO4)2 to changes in the bond distances and angles of the coordination sphere of iron(II), hinting at a stronger σ donation of ligand Z in comparison to ligand M. The UV/vis spectra of both complexes are solved by means of the multiconfigurational wave-function-based method CASPT2 and confirm their different spin multiplicities at room temperature, as observed in the Mössbauer spectra. Calculations show larger stabilization of the singlet state in [Fe(Z)3]2+ than in [Fe(M)3]2+, stemming from the slightly stronger ligand field of the former (506 cm-1 in the singlet). This relatively weak effect is indeed capable of changing the spin multiplicity of the complexes and causes the appearance of the spin transition in the M complex.

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