In Vitro Evaluation and In Silico Calculations of the Antioxidant and Anti-Inflammatory Properties of Secondary Metabolites from Leonurus sibiricus L. Root Extracts

Leonurus sibiricus L. has great ethnobotanical and ethnomedicinal significance. This study aimed to assess the antioxidant and anti-inflammatory properties of Leonurus sibiricus L. transgenic roots extracts transformed by Rhizobium rhizogenes, with and without the AtPAP1 transcriptional factor. The study determined the total phenolic and flavonoid contents, as well as in vitro antioxidant assays, including hydrogen peroxide and nitric oxide scavenging activity. In addition, in silico computational studies and molecular docking were conducted to evaluate the antioxidant and anti-inflammatory potential of the identified compounds. The ligands were docked to NADPH oxidase, cyclooxygenase 2,5-lipoxygenase, inducible nitric synthase and xanthine oxidase: enzymes involved in the inflammatory process. The total phenolic and flavonoid contents ranged from 85.3 ± 0.35 to 57.4 ± 0.15 mg/g GAE/g and 25.6 ± 0.42 to 18.2 ± 0.44 mg/g QUE/g in hairy root extracts with and without AtPAP1, respectively. H2O2 scavenging activity (IC50) was found to be 29.3 µg/mL (with AtPAP1) and 37.5 µg/mL (without AtPAP1 transcriptional factor), and NO scavenging activity (IC50) was 48.0 µg/mL (with AtPAP1) and 68.8 µg/mL (without AtPAP1 transcriptional factor). Leonurus sibiricus L. transformed root extracts, both with and without AtPAP1, are a source of phytochemicals belonging to different classes of molecules, such as flavonoids (catechin and rutin), phenolic compounds (caffeic acid, coumaric acid, chlorogenic acid, ferulic acid) and phenylpropanoid (verbascoside). Among the radicals formed after H removal from the different -OH positions, the lowest bond dissociation enthalpy was observed for rutin (4'-OH). Rutin was found to bind with cyclooxygenase 2, inducible nitric synthases and xanthine oxidase, whereas chlorogenic acid demonstrated optimal binding with 5-lipoxygenase. Therefore, it appears that the Leonurus sibiricus L. transformed root extract, both with and without the AtPAP1 transcriptional factor, may serve as a potential source of active components with antioxidant and anti-inflammatory potential; however, the extract containing AtPAP1 demonstrates superior activities. These properties could be beneficial for human health.

Model Compounds for Intermediates and Transition States in Sonogashira and Negishi Coupling: d8-d10 Bonds in Large Heterobimetallic Complexes Are Weaker than Computational Chemistry Predicts

We report an experimental study, with accompanying DFT calculations, on a series of heterobimetallic complexes with Pd(II) and Cu(I), Ag(I), or Au(I). The isolable pincer complexes are models for the intermediates and transition state for the transmetalation step in Sonogashira and Negishi coupling reactions, among which, according to the DFT calculations, only the transition state has the two metal centers within bonding distance. Furthermore, we report a substituted version of an analogous heterobimetallic complex in which a competing dissociation sets an upper-bound on the strength of the d⁸-d¹⁰ metal-metal bond. Analysis of the structures in the solid state and in solution, and the competitive dissociation experiment in the gas phase, indicate that the dispersion-corrected DFT method used in the study appears to overestimate the strength of the metal-metal interaction, thus distorting the shape of the computed potential energy surface systematically for transmetalation.

Calculation of Metallocene Ionization Potentials via Auxiliary Field Quantum Monte Carlo: Toward Benchmark Quantum Chemistry for Transition Metals

The accurate ab initio prediction of ionization energies is essential to understanding the electrochemistry of transition metal complexes in both materials science and biological applications. However, such predictions have been complicated by the scarcity of gas phase experimental data, the relatively large size of the relevant molecules, and the presence of strong electron correlation effects. In this work, we apply all-electron phaseless auxiliary-field quantum Monte Carlo (ph-AFQMC) utilizing multideterminant trial wave functions to six metallocene complexes to compare the computed adiabatic and vertical ionization energies with experimental results. We find that ph-AFQMC yields mean absolute errors (MAEs) of 1.69 ± 1.02 kcal/mol for the adiabatic energies and 2.85 ± 1.13 kcal/mol for the vertical energies. We also carry out density functional theory (DFT) calculations using a variety of functionals, which yields MAEs of 3.62-6.98 kcal/mol and 3.31-9.88 kcal/mol, as well as one variant of localized coupled cluster calculations (DLPNO-CCSD(T₀) with moderate PNO cutoffs), which has MAEs of 4.96 and 6.08 kcal/mol, respectively. We also test the reliability of DLPNO-CCSD(T₀) and DFT on acetylacetonate (acac) complexes for adiabatic energies measured in the same manner experimentally, and we find higher MAEs, ranging from 4.56 to 10.99 kcal/mol (with a different ordering) for DFT and 6.97 kcal/mol for DLPNO-CCSD(T₀). Finally, by utilizing experimental solvation energies, we show that accurate reduction potentials in solution for the metallocene series can be obtained from the AFQMC gas phase results.

A Study of NbMo and NbMo- by Anion Photoelectron Spectroscopy

Photoelectron spectra of the niobium-molybdenum diatomic anion, obtained at 488 and 514 nm, display vibrationally resolved transitions from the ground state and one excited electronic state of the anion to the ground state and one excited electronic state of the neutral molecule. The electron affinity of NbMo is measured to be 1.130 ± 0.005 eV. Its ²Δ_3/2 spin-orbit component is observed to lie 870 ± 20 cm^-1 above its previously identified ²Δ_5/2 ground state. For ⁹³Nb⁹⁸Mo, vibrational energies measured for levels up to v = 4 for the ²Δ_5/2 and ²Δ_3/2 states give harmonic frequency and anharmonicity constant values of ω_e = 492 ± 12 cm^-1 and ω_ex_e = 8.0 ± 3.2 cm^-1, the former value corresponding to a force constant of 6.80 ± 0.35 mdyn/Å. These two vibrational parameters suggest a bond dissociation energy that is too low by at least a factor of 3, indicating that the ground state potential energy curve of NbMo deviates markedly from a Morse potential at higher energies. An excited electronic state of NbMo, assigned as a ²Σ⁺ state, is observed at 2900 ± 25 cm^-1 (T₀). Vibrational energies up to v = 8 in this excited state give values of ω_e = 544 ± 8 cm^-1 and ω_ex_e = 1.9 ± 1.2 cm^-1 for ⁹³Nb⁹⁸Mo. The former value corresponds to a high vibrational force constant of 8.30 ± 0.25 mdyn/Å. Both doublet states of the neutral molecule are accessed from the anion ground state, which is assigned as ¹Σ⁺. For the ⁹³Nb⁹⁸Mo^- anion, the fundamental vibrational frequency (ΔG_1/2) is 484 ± 15 cm^-1. Electron affinity data indicate that the bond dissociation energy of NbMo^- is 0.213 ± 0.005 eV greater than that of neutral NbMo, whose previously reported value then gives D₀ = 4.85 ± 0.27 eV for the anion. An excited state of the anion lying 3050 ± 25 cm^-1 (T₀) above its ground state is assigned as ³Δ, and the energies of its spin-orbit components above the ³Δ₃ lowest energy level are measured to be 450 ± 20 cm^-1 (³Δ₂) and 1100 ± 20 cm^-1 (³Δ₁). Their uneven spacing suggests that the energy of the ³Δ₂ level is lowered by interaction with a higher energy Ω = 2 anion state. The vibrational frequency (ΔG_1/2) for the ³Δ₁ and ³Δ₂ states is measured to be 433 ± 20 cm^-1. Bond length differences among the observed states are estimated from Franck-Condon fits to vibrational band intensity profiles. When combined with the previously reported NbMo bond length, these provide bond length estimates for the ground state of the anion (1.940 ± 0.025 Å) and for the observed excited states. These species offer extreme examples of multiple metal-metal bonding, with formal bond orders of 5¹/₂ for the ²Δ ground and ²Σ⁺ excited doublet states of NbMo, 6 for the singlet ground state of the anion, and 5 for its low-lying triplet state. The relationships among their bonding properties and those of related multiply bonded transition metal dimers are discussed.

Predicting Bond Dissociation Energies and Bond Lengths of Coordinatively Unsaturated Vanadium-Ligand Bonds

Understanding the electronic structure of coordinatively unsaturated transition-metal compounds and predicting their physical properties are of great importance for catalyst design. Bond dissociation energy D_e and bond length r_e are two of the fundamental quantities for which good predictions are important for a successful design strategy. In the present work, recent experimentally measured bond energies and bond lengths of VX diatomic molecules (X = C, N, S) are used as a gauge to consider the utility of a number of electronic structure methods. Single-reference methods are one focus because of their efficiency and utility in practical calculations, and multireference configuration interaction (MRCISD) methods and a composite coupled cluster (CCC) method are a second focus because of their potential high accuracy. The comparison is especially challenging because of the large multireference M diagnostics of these molecules, in the range 0.15-0.19. For the single-reference methods, Kohn-Sham density functional theory (KS-DFT) has been tested with a variety of approximate exchange-correlation functionals. Of these, MOHLYP provides the bond dissociation energies in best agreement with experiments, and BLYP provides the bond lengths that are in best agreement with experiments; but by requiring good performance for both the D_e and r_e of the vanadium compounds, MOHLYP, MN12-L, MGGA_MS1, MGGA_MS0, O3LYP, and M06-L are the most highly recommended functionals. The CCC calculations include up to connected pentuple excitations for the valence electrons and up to connected quadruple excitations for the core-valence terms; this results in highly accurate dissociation energies and good bond lengths. Averaged over the three molecules, the mean unsigned deviation of CCC bond energies from experimental ones is only 0.4 kcal/mol, demonstrating excellent convergence of theory and experiments.

Bond dissociation energies of FeSi, RuSi, OsSi, CoSi, RhSi, IrSi, NiSi, and PtSi

Resonant two-photon ionization spectroscopy has been used to investigate the spectra of the diatomic late transition metal silicides, MSi, M = Fe, Ru, Os, Co, Rh, Ir, Ni, and Pt, in the vicinity of the bond dissociation energy. In these molecules, the density of vibronic states is so large that the spectra appear quasicontinuous in this energy range. When the excitation energy exceeds the ground separated atom limit, however, a new decay process becomes available-molecular dissociation. This occurs so rapidly that the molecule falls apart before it can absorb another photon and be ionized. The result is a sharp drop to the baseline in the ion signal, which we identify as occurring at the thermochemical 0 K bond dissociation energy, D₀. On this basis, the measured predissociation thresholds provide D₀ = 2.402(3), 4.132(3), 4.516(3), 2.862(3), 4.169(3), 4.952(3), 3.324(3), and 5.325(9) eV for FeSi, RuSi, OsSi, CoSi, RhSi, IrSi, NiSi, and PtSi, respectively. Using thermochemical cycles, the enthalpies of formation of the gaseous MSi molecules are derived as 627(8), 700(10), 799(10), 595(8), 599(8), 636(10), 553(12), and 497(8) kJ/mol for FeSi, RuSi, OsSi, CoSi, RhSi, IrSi, NiSi, and PtSi, respectively. Likewise, combining these results with other data provides the ionization energies of CoSi and NiSi as 7.49(7) and 7.62(7) eV, respectively. Chemical bonding trends among the diatomic transition metal silicides are discussed.

How well can density functional theory and pair-density functional theory predict the correct atomic charges for dissociation and accurate dissociation energetics of ionic bonds?

The accuracy of density functional theory (DFT) is often judged by predicted dissociation energies, but one should also consider charge densities as illustrated here for dissociation of heteronuclear diatomic molecules, including ionic bonds for which local density functionals yield erroneous results. Some hybrid density functionals with 100% exact exchange in Kohn-Sham DFT and the local functionals in multiconfiguration pair-density functional theory give relatively acurate dissociation energies for NaCl, and they correctly yield uncharged dissociated atoms.

Self-Interaction Error in Density Functional Theory: An Appraisal

Self-interaction error (SIE) is considered to be one of the major sources of error in most approximate exchange-correlation functionals for Kohn-Sham density-functional theory (KS-DFT), and it is large with all local exchange-correlation functionals and with some hybrid functionals. In this work, we consider systems conventionally considered to be dominated by SIE. For these systems, we demonstrate that by using multiconfiguration pair-density functional theory (MC-PDFT), the error of a translated local density-functional approximation is significantly reduced (by a factor of 3) when using an MCSCF density and on-top density, as compared to using KS-DFT with the parent functional; the error in MC-PDFT with local on-top functionals is even lower than the error in some popular KS-DFT hybrid functionals. Density-functional theory, either in MC-PDFT form with local on-top functionals or in KS-DFT form with some functionals having 50% or more nonlocal exchange, has smaller errors for SIE-prone systems than does CASSCF, which has no SIE.

Multiconfiguration Pair-Density Functional Theory Is Free From Delocalization Error

Delocalization error has been singled out by Yang and co-workers as the dominant error in Kohn-Sham density functional theory (KS-DFT) with conventional approximate functionals. In this Letter, by computing the vertical first ionization energy for well separated He clusters, we show that multiconfiguration pair-density functional theory (MC-PDFT) is free from delocalization error. To put MC-PDFT in perspective, we also compare it with some Kohn-Sham density functionals, including both traditional and modern functionals. Whereas large delocalization errors are almost universal in KS-DFT (the only exception being the very recent corrected functionals of Yang and co-workers), delocalization error is removed by MC-PDFT, which bodes well for its future as a step forward from KS-DFT.

Modeling σ-Bond Activations by Nickel(0) Beyond Common Approximations: How Accurately Can We Describe Closed-Shell Oxidative Addition Reactions Mediated by Low-Valent Late 3d Transition Metal?

Accurate modelings of reactions involving 3d transition metals (TMs) are very challenging to both ab initio and DFT approaches. To gain more knowledge in this field, we herein explored typical σ-bond activations of H-H, C-H, C-Cl, and C-C bonds promoted by nickel(0), a low-valent late 3d TM. For the key parameters of activation energy (ΔE^‡) and reaction energy (ΔE_R) for these reactions, various issues related to the computational accuracy were systematically investigated. From the scrutiny of convergence issue with one-electron basis set, augmented (A) basis functions are found to be important, and the CCSD(T)/CBS level with complete basis set (CBS) limit extrapolation based on augmented double-ζ and triple-ζ basis pair (ADZ and ATZ), which produces deviations below 1 kcal/mol from the reference, is recommended for larger systems. As an alternative, the explicitly correlated F12 method can accelerate the basis set convergence further, especially after its CBS extrapolations. Thus, the CCSD(T)-F12/CBS(ADZ-ATZ) level with computational cost comparable to the conventional CCSD(T)/CBS(ADZ-ATZ) level, is found to reach the accuracy of the conventional CCSD(T)/A5Z level, which produces deviations below 0.5 kcal/mol from the reference, and is also highly recommendable. Scalar relativistic effects and 3s3p core-valence correlation are non-negligible for achieving chemical accuracy of around 1 kcal/mol. From the scrutiny of convergence issue with the N-electron basis set, in comparison with the reference CCSDTQ result, CCSD(T) is found to be able to calculate ΔE^‡ quite accurately, which is not true for the ΔE_R calculations. Using highest-level CCSD(T) results of ΔE^‡ in this work as references, we tested 18 DFT methods and found that PBE0 and CAM-B3LYP are among the three best performing functionals, irrespective of DFT empirical dispersion correction. With empirical dispersion correction included, ωB97XD is also recommendable due to its improved performance.

Comparative Study of Nonhybrid Density Functional Approximations for the Prediction of 3d Transition Metal Thermochemistry

The utility of several nonhybrid density functional approximations (DFAs) is considered for the prediction of gas phase enthalpies of formation for a large set of 3d transition metal-containing molecules. Nonhybrid DFAs can model thermochemical values for 3d transition metal-containing molecules with accuracy comparable to that of hybrid functionals. The GAM-generalized gradient approximation (GGA); the TPSS, M06-L, and MN15-L meta-GGAs; and the Rung 3.5 PBE+ΠLDA(s) DFAs all give root-mean-square deviations below that of the widely used B3LYP hybrid. Modern nonhybrid DFAs continue to show utility for transition metal thermochemistry.