Effect of porphyrin ligands on the catalytic CH4 oxidation activity of monocationic μ-nitrido-bridged iron porphyrinoid dimers by using H2O2 as an oxidant

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.

Stereochemistry-Dependent Labeling of Organelles with a Near-Infrared-Emissive Phosphorus-Bridged Rhodamine Dye in Live-Cell Imaging

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.

First-principles studies of enhanced oxygen reduction reactions on graphene- and nitrogen-doped graphene-coated platinum surfaces

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.

Close Stacking of Antiaromatic Ni(II) Norcorrole Originating from a Four-Electron Multicentered Bonding Interaction

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.

Local Oxidation States in {FeNO}6-8 Porphyrins: Insights from DMRG/CASSCF-CASPT2 Calculations

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.

The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry

The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.

Insight into Scattering Mechanisms and Transport Properties of AgCuS for Flexible Thermoelectric Applications

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.

Unraveling the Spin-State Energetics of FeN4 Complexes with Ab Initio Methods

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.

Evaluation of CH4 Oxidation Activity of High-Valent Iron-Oxo Species of A μ-Nitrido-Bridged Heterodimer of Iron Porphycene and Iron Phthalocyanine

A μ-nitrido-bridged dimer of iron phthalocyanine is one of the most potent molecule-based CH4 oxidation catalysts reported to date. The reactive intermediate is a high-valent iron-oxo species generated through reaction...

A DMRG/CASPT2 Investigation of Metallocorroles: Quantifying Ligand Noninnocence in Archetypal 3d and 4d Element Derivatives

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.

Combination of a Voronoi-Type Complex Absorbing Potential with the XMS-CASPT2 Method and Pilot Applications

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 ⁴Π_u and ²Π_u 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 ⁴Π_u and ²Π_u resonance states of N₂^- including their ³Σ_u⁺ and ³Δ_u parent states. Three of the involved states (²Π_u, ³Σ_u⁺, and ³Δ_u) possess multireference character, and CAP/XMS-CASPT2 can easily describe these states with a relatively modest active space.

Polarization consistent basis sets using the projector augmented wave method: a renovation brought by PAW into Gaussian basis sets

A new family of polarization consistent basis set, combined with the projector augmented wave method, was introduced. The basis sets are compact and have good performance as compared to conventional all-electron basis sets in DFT calculations.

Electronic Structure of N-Bridged High-Valent Diiron-Oxo

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 Fe^V -Fe^IV 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.

Understanding the Reactivity of Mn-Oxo Porphyrins for Substrate Hydroxylation: Theoretical Predictions and Experimental Evidence Reconciled

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 O^2-) 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).

Low-Lying Electromeric States in Chloro-Ligated Iron(IV)-Oxo Porphyrin as a Model for Compound I, Studied with Second-Order Perturbation Theory Based on Density Matrix Renormalization Group

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 Fe^IVO ground state and, more importantly, a thermally accessible doublet Fe^VO 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.

Limits of Coupled-Cluster Calculations for Non-Heme Iron Complexes

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.

Reaction Mechanism of [NiFe] Hydrogenase Studied by Computational Methods

[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.

Toward Highly Accurate Spin State Energetics in First-Row Transition Metal Complexes: A Combined CASPT2/CC Approach

In previous work on the performance of multiconfigurational second-order perturbation theory (CASPT2) in describing spin state energetics in first-row transition metal systems [ Pierloot et al. J. Chem. Theory Comput. 2017 , 13 , 537 - 553 ], we showed that standard CASPT2 works well for valence correlation but does not describe the metal semicore (3s3p) correlation effects accurately. This failure is partially responsible for the well-known bias toward high-spin states of CASPT2. In this paper, we expand our previous work and show that this bias could be partly removed with a combined CASPT2/CC approach: using high-quality CASPT2 with extensive correlation-consistent basis sets for valence correlation and low-cost CCSD(T) calculations with minimal basis sets for the metal semicore (3s3p) correlation effects. We demonstrate that this approach is efficient by studying the spin state energetics of a series of iron complexes modeling important intermediates in oxidative catalytic processes in chemistry and biochemistry. On the basis of a comparison with bare CCSD(T) results from this and previous work, the average error of the CASPT2/CC approach is estimated at around 2 kcal mol^-1 in favor of high spin states.

The dioxygen adducts of iron and manganese porphyrins: electronic structure and binding energy

The electronic structures of adducts of O₂ and metal porphyrins were thoroughly investigated by highly accurate DMRG-CASPT2.

H2binding to the active site of [NiFe] hydrogenase studied by multiconfigurational and coupled-cluster methods

CCSD(T) and DMRG-CASPT2 calculations show that H₂prefers to bind to Ni rather than to Fe in [NiFe] hydrogenase.

Theoretical Study of the Dissociation Energy of First-Row Metallocenium Ions

The bond dissociation energy of a series of metallocenium ions, i.e., the energy difference of the reaction MCp2(+) → MCp(+) + Cp· (with M = Ti, V, Cr, Mn, Fe, Co, and Ni), was studied by means of multiconfigurational perturbation theory (CASPT2, RASPT2, NEVPT2) and restricted coupled cluster theory (CCSD(T)). From a comparison between the results obtained from these different methods, and a detailed analysis of their treatment of electron correlation effects, a set of MCp(+)-Cp binding energies are proposed with an accuracy of 5 kcal/mol. The computed results are in good agreement with the experimental data measured by threshold photoelectron photoion coincidence (TPEPICO) spectroscopy but disagree with the more recent threshold collision-induced dissociation (TCID) experiments.