Toward Reliable DFT Investigations of Mn-Porphyrins through CASPT2/DFT Comparison

Influence of Cysteine 440 on the Active Site Properties of 3-Deoxy-d-Arabino-Heptulosonate 7-Phosphate Synthase in Mycobacterium tuberculosis (MtDAHPS)

The shikimate pathway, which produces aromatic amino acids and key intermediates, is critical to the viability of the tuberculosis-causing pathogen Mycobacterium tuberculosis. The enzyme 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAHPS) catalyzes the first committed step of this pathway and possesses regulatory functions. Its active site contains two cysteinyls: one (Cys₈₇) bound to a metal ion, while the other (Cys₄₄₀) is in proximity to the first but is located on a connecting loop. This arrangement seemingly appeared as a disulfide linkage. However, Cys₄₄₀ is not metal binding, and its positioning indicates that it could collapse the disulfide linkage. Hence, its potential role may be more than simply structural support of the active site fold. Using a multiscale computational approach, molecular dynamics (MD) simulations, and DFT-based calculations, the influence of Cys₄₄₀ on the active site properties has been investigated. MD simulations reveal an unusually long disulfide bond, more than 3.0 Å, whereas DFT calculations identified two stable active site conformers in the triplet and quintet spin states. Analysis of group spin density distribution identified antiferromagnetic coupling in each conformer, which suggests their relatively low potential energy and stable conformations. The conformer in the triplet spin state could favor enzyme reactivity due to its low HOMO-LUMO energy gap. In addition, reduction of the Cys₄₄₀ thiolate group results in collapse of the active site metal-ligand configuration with large exothermicity. Hence, Cys₄₄₀ could activate and inactivate the enzyme. For the first time, the study revealed the role of Cys₄₄₀ as being vital for the catalytic activity of the enzyme rather than solely for the structural stabilization of its active site. Thus, the findings may lead to a novel basis for antituberculosis drug design and development that would disrupt the contributions of the Cys₄₄₀.

Computational study of ground-state properties of μ2 -bridged group 14 porphyrinic sandwich complexes

The structural properties of μ₂ -bridged porphyrinic double-decker complexes are investigated and the influence of various ligands, metals, substituents, and bridging atoms on the dominant structural motif is elucidated. A variety of quantum chemical methods including semiempirical (SQM) methods and density functional theory (DFT) is assessed for the calculation of ecliptic and staggered conformational energies. Local coupled cluster (DLPNO-CCSD(T1)) data are generated for reference. The r² SCAN-3c composite scheme as well as the B2PLYP-D4/def2-QZVPP approach are identified as reliable methods. Energy decomposition analyses (EDA) and localized molecular orbital analyses (LMO) are used to investigate the bonding situation and the nature of the inter-ligand interaction energy underlining the crucial role of attractive London dispersion interactions. Targeted modification of the bridging atom, e.g., by replacing O^2- by S^2- is shown to drastically change the major structural features of the investigated complexes. Further, the influence of different substituents of varying size at the phthalocyanine ligand regarding the dominant conformation is described.

Characterization of the UV-Visible absorption spectra of manganese(III) porphyrins with time-dependent density functional theory calculations

Mn(III) porphyrins display a unique UV–Vis spectrum: compared to the free-base and other metalloporphyrins, a strong red shift of the Soret-band and several extra bands can be observed in their spectra. To understand this behavior, we have recorded the UV–Vis spectra of differently substituted water-soluble Mn(III) porphyrins and conducted extensive theoretical investigations using time-dependent density functional theory. The calculated optical transitions, using the O3LYP functional, agree well with the measured absorption bands. According to the spectral interpretation, the Soret-band involves a mixture of L–L and ligand-to-metal charge transfer excitations, while the Q-bands and the higher-energy bands in the UV region correspond to pure LMCT as well as to ligand to metal-ligand mixed orbital excitations. The impact of the explicit and implicit water solvent on the spectral features is also discussed.

Theoretical modeling of the singlet-triplet spin transition in different Ni(II)-diketo-pyrphyrin-based metal-ligand octahedral complexes

The structural stability, charge transfer effects and strength of the spin-orbit couplings in different Ni(ii)-ligand complexes have been studied at the DFT (B3LYP and CAM-B3LYP) and coupled cluster (DLPNO-CCSD(T)) levels of theory. Accordingly, two different, porphyrin- and diketo-pyrphyrin-based four-coordination macrocycles as planar ligands as well as pyridine (or pyrrole) and mesylate anion molecular groups as vertical ligands were considered in order to build metal-organic complexes with octahedral coordination configurations. For each molecular system, the identification of equilibrium geometries and the intersystem crossing (the minimum energy crossing) points between the potential energy surfaces of the singlet and triplet spin states is followed by computing the spin-orbit couplings between the two spin states. Structures, based on the diketo-pyrphyrin macrocycle as the planar ligand, show stronger six-coordination metal-organic complexes due to the extra electrostatic interaction between the positively charged central metal cation and the negatively charged vertical ligands. The results also show that the magnitude of the spin-orbit coupling is influenced by the atomic positions of deprotonations of the ligands, and implicitly the direction of the charge transfer between the ligand and the central metal ion.

Theoretical Study on Electronic Structural Properties of Catalytically Reactive Metalloporphyrin Intermediates

Metalloporphyrins have attracted great attention in the potential application of biomimetic catalysis. Especially, they were widely investigated as green catalysts in the chemical oxidation of various hydrocarbons through the catalytic activation of molecular oxygen. The structural properties of active central metal ions were reported to play a decisive role in catalytic activity. However, those delicate structural changes are difficult to be experimentally captured or elucidated in detail. Herein, we explored the electronic structural properties of metalloporphyrins (metal porphyrin (PMII, PMIIICl)) and their corresponding catalytically active intermediates (metal(III)-peroxo(PMIII-O2), metal(III)-hydroperoxo(PMIII-OH), and metal(IV)-oxo(PMIV=O), (M=Fe, Mn, and Co)) through the density functional theory method. The ground states of these intermediates were determined based on the assessment of relative energy and the corresponding geometric structures of ground states also further confirmed the stability of energy. Furthermore, our analyses of Mulliken charges and frontier molecular orbitals revealed the potential catalytic behavior of reactive metalloporphyrin intermediates.

Structure, Properties, and Reactivity of Porphyrins on Surfaces and Nanostructures with Periodic DFT Calculations

Porphyrins are fascinating molecules with applications spanning various scientific fields. In this review we present the use of periodic density functional theory (PDFT) calculations to study the structure, electronic properties, and reactivity of porphyrins on ordered two dimensional surfaces and in the formation of nanostructures. The focus of the review is to describe the application of PDFT calculations for bridging the gaps in experimental studies on porphyrin nanostructures and self-assembly on 2D surfaces. A survey of different DFT functionals used to study the porphyrin-based system as well as their advantages and disadvantages in studying these systems is presented.

Hydration of Closely Related Manganese and Magnesium Porphyrins in Aqueous Solutions: Ab Initio Quantum Mechanical Charge Field Molecular Dynamics Simulation Study

To the best of our knowledge, the current study based on ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) is the first to explore the difference in the hydration behavior between Mn(II)- and Mg(II)-associated porphyrins (Mn(II)-POR and Mg(II)-POR) in aqueous solution. The simulation study highlights similar and dissimilar characteristics of the structural, dynamical, and thermodynamical properties of these closely related metals bound to porphyrins in aqueous solution. The structural analysis is based on radial and angular distribution functions, coordination number distributions, and angular-radial distributions. Both hydrated systems demonstrate similar pentacoordinated structures formed via the axial coordination of one water molecule to the metal ion in addition to the four nitrogen atoms of the porphyrin ring. However, in the case of Mn(II)-POR, the formation of a distorted square pyramidal geometry was observed. It was envisaged as a weak coordination of the water molecule to the Mn(II) atom and thus higher atomic fluctuation for all atoms in contrast to that for the hydrated Mg(II)-POR. The dynamical data in terms of the mean residence times, velocity autocorrelation function, free energy, and other parameters revealed the difference in the metal binding effect because the Mn(II) atom was observed to inhibit H-bond formation more than the presence of Mg(II) atoms in the core of the porphyrin. The current study thus highlights the significant differences in the structural and dynamical properties of Mn(II)- and Mg(II)-associated porphyrin systems.

Benchmarking quantum chemistry methods for spin-state energetics of iron complexes against quantitative experimental data

The accuracy of relative spin-state energetics predicted by selected quantum chemistry methods: coupled cluster theory at the CCSD(T) level, multiconfigurational perturbation theory (CASPT2, NEVPT2), multireference configuration interaction at the MRCISD+Q level, and a number of DFT methods, is quantitatively evaluated by comparison with the experimental data of four octahedral iron complexes. The available experimental data, either spin-forbidden transition energies or spin crossover enthalpies, are corrected for relevant environmental effects in order to derive the quantitative benchmark set of iron spin-state energetics. Comparison of theory predictions with the resulting reference data: (1) validates the high accuracy of the CCSD(T) method, particularly when based on Kohn-Sham orbitals, giving the maximum error below 2 kcal mol-1 and the mean absolute error (MAE) below 1 kcal mol-1; (2) corroborates the tendency of CASPT2 to systematically overstabilize higher-spin states by up to 5.5 kcal mol-1; (3) confirms that the latter problem is partly remedied by the recently proposed CASPT2/CC approach [Phung et al., J. Chem. Theory Comput., 2018, 14, 2446-2455]; (4) demonstrates that NEVPT2 performs worse than CASPT2, by giving errors up to 7 kcal mol-1; (5) shows that the accuracy of MRCISD+Q spin-state energetics strongly depends on the size-consistency correction: the Davidson-Silver and Pople corrections perform best (MAE < 3 kcal mol-1), whereas the standard Davidson correction is not recommended (MAE of 7 kcal mol-1). Only a few DFT methods (including the best performing ones identified in this study: B2PLYP-D3 and OPBE) are able to provide a balanced description of the spin-state energetics for all four studied iron complexes simultaneously, corroborating the non-universality problem of approximate density functionals.

The Importance of the MM Environment and the Selection of the QM Method in QM/MM Calculations: Applications to Enzymatic Reactions

In this chapter, we discuss the influence of an anisotropic protein environment on the reaction mechanisms of saccharopine reductase and uroporphyrinogen decarboxylase, respectively, via the use of a quantum mechanical and molecular mechanical (QM/MM) approach. In addition, we discuss the importance of selecting a suitable DFT functional to be used in a QM/MM study of a key intermediate in the mechanism of 8R-lipoxygenase, a nonheme iron enzyme. In the case of saccharopine reductase, while the enzyme utilizes a substrate-assisted catalytic pathway, it was found that only through treating the polarizing effect of the active site, via the use of an electronic embedding formalism, was agreement with experimental kinetic data obtained. Similarly, in the case of uroporphyrinogen decarboxylase, the effect of the protein environment on the catalytic mechanism was found to be such that the calculated rate-limiting barrier is in good agreement with related experimentally determined values for the first decarboxylation of the substrate. For 8R-lipoxygenase, it was found that the geometries and energies of the multicentered open-shell intermediate complexes formed during the mechanism are quite sensitive to the choice of the density functional theory method. Thus, while density functional theory has become the method of choice in QM/MM studies, care must be taken in the selection of a particular high-level method.

Difficulties in the ab initio description of electron transport through spin filters

Spin-transport calculations present certain difficulties which are sometimes overlooked when using density-functional theory (DFT) to analyze and predict the behavior of molecular-based devices. We analyze and give examples of some caveats of spintronic calculations using DFT. We first describe how the broken-symmetry problem of DFT can cause serious problems in the evaluation of the spin polarization of electron currents. Next, we signal the low-energy scale of magnetic excitations, which makes them ubiquitous at already rather small biases. The existence of excitations in spin transport has catastrophic consequences in the reliability of the usual transport calculations. Finally, we compare DFT and configuration-interaction calculations of a ferrocene-based double decker that has been heralded as a possible spin-filter, and we cast a word of caution when we show that DFT is qualitatively wrong in the description of both the ground state and the excited states of ferrocene double deckers.

Watching energy transfer in metalloporphyrin heterodimers using stimulated X-ray Raman spectroscopy

Understanding the excitation energy transfer mechanism in multiporphyrin arrays is key for designing artificial light-harvesting devices and other molecular electronics applications. Simulations of the stimulated X-ray Raman spectroscopy signals of a Zn/Ni porphyrin heterodimer induced by attosecond X-ray pulses show that these signals can directly reveal electron-hole pair motions. These dynamics are visualized by a natural orbital decomposition of the valence electron wavepackets.